Let us start with the fact that IMAP can never be a local archive. Consider it a local cache, but in no way is it an archive. Delete the mail on the server and Thunderbird will also delete the mail. Loose the account t=and Thunderbird will delete even the folder names leaving an empty inbox.

I am guessing that the other account is actuially a renamed local folders account as it has an outbox folder (you should only see that in "Local Folders"

Mail in Local folders can be considered an archive, but like any local storage requires local backup as well.

You might try deleting the foldertree.json file and folderchache.json from your profile folder without Thunderbird running and see if that helps with the duplication.

Thank you for your response, Matt. You are correct and I apologize. I do understand the difference between IMAP and POP and I muddied the waters. Again, my apologies. I am actually only interested in the POP account for this issue.

I will try your suggestion, thank you. However, before I do so, is there any recommended way to 'backup' my Thunderbird files in case I make a misstep? I'm guessing making a copy of my ~/Library/Thunderbird/Profiles/<Profile name> directory. However, would like to be sure.

Again, thank you for your response. rOot

I gave the suggestion a try, removing the foldertree.json and folderchache.json files from my profile. However, the only change this did, is it renamed several folders in what I can only guess is some random manner. (Please see attached screen grab.)

I feel like this is some type of indexing issue, that Thunderbird has lost track of the folders, sub-folders and messages and needs to re-index... or something of that nature.

Thanks for any thoughts or suggestions!

Not having much luck rebuilding the email database (?? not sure what to call it). I believe I still have all the emails in my profile, but I don't know how to force Thunderbird to rebuilt it's index of messages. Everything I seem to find is about search, not the emails themselves. Wondering if anyone has any suggestions?

is there any recommended way to 'backup' my Thunderbird files in case I make a misstep? I'm guessing making a copy of my ~/Library/Thunderbird/Profiles/<Profile name> directory. However, would like to be sure.

Yes, you can copy that profile folder manually to a safe location. If your profile is less than two GB, you could also use Tools > Export.

Even better is making regular back-ups of your whole drive if you are not doing it already. Do you have back-ups? You may need them if you cannot get everything back the way it should be.

I don't believe that I can help much with the main problem, but I wonder if posting a screen capture of the folders in question would help someone else. I'm curious about how the folders are named in the file system and how large they are.

You might try right clicking on a folder that seems to be empty but should not be, then on "Properties", and "Repair folder".

Hello all. Rick, thank you for your suggestions. I apologize for not posting anything for some time. Your point of backups is well taken. I have become slack in my aged years and complaisant in the Apple world so when Retrospect went under, I stopped worrying about them. Here I am bitten by my own laziness. I have been doing a bunch of basic Googling on my issue and have tried the following: - Using the "Repair Folder" option in Folder Properties. No change. - Manually deleting all the .msf files in my ~/Library/Thunderbird/ folders. No change. - Using Tools -> Export to a zip file and attempting to re-import profiles. I did without removing my profiles folder and also with deleting my profiles folder from ~/Library/Thunderbird. In the former case, no change. In the latter case, no duplicate folders but no emails in the folders in question. - Deleting ~/Library/Thunderbird/global-messages-db.sqlite and restarting the app. No change. - Deleting ~/Library/Thunderbird/folderCache.json and restarting the app. Folders were correct, but, again, no mail in them.

I feel as if something is keeping the application from re-indexing the mail files. The document files that hold the actual message, still have the messages, it's just that Thunderbird refuses to see or show them.

To answer Rick's question about the folder naming...

- In my ~/Library/Thunderbird/default.emc/Mail/Local Folders I have a folder called rOotboy's email which has all the sub-folders of messages under that. All those names correspond to what you can see in my previous screen grabs. Except for new folders that have numbers rather than names. That you can see in the second screen grab above.

If anyone has ANY suggestions or thoughts, I'd be very grateful to hear them. As I say, it's as if Thunderbird will not re-index the messages and I have no idea why.

This all happened shortly after a Thunderbird update, just before v140.1.0esr (aarch64). I do not know if it's related but that's the only change I know of from working to not working.

What are the sizes of the mbox files in the macOS file system?

Can you post a screenshot showing them?

Not sure they are mbox. Mac OS 26 doesn't give them a file type.

There are a couple largest ones but nothing crazy. I've put a file system screen shot of some on this post.

Curious what you hope to see?

They are mbox files without an extension.

I wanted to confirm that the files were big enough to hold messages and that we weren't just hoping that your messages were still present. I see that you probably have 3.3 GB of messages. That is re-assuring.

I don't know what is best here, so I'm hoping that other people will join the discussion. But if this were my computer, I would probably do this:

1. Close Thunderbird.
2. Make a copy of my whole profile on an external disk for back-up.
3. Open Thunderbird. Help > Troubleshooting information > about:profiles, create a new profile.
4. Launch the new profile and set up the local folders account. (I don't know what must be done here, if anything. I also don't know if you can avoid or how to avoid setting up at least one other account. You will probably figure that out.)
5. Close both Thunderbird instances.
6. Go to ~/Library/Thunderbird/default.emc/Mail/Local Folders, expand one of those disclosure triangles (say, on "Current.sbd") to reveal mbox files in the folder, and copy (not move) one or more mbox files to /Mail/Local Folders of your new profile. MBOX files in Thunderbird have no exension, not an msf, not an sbd.
7. Launch Thunderbird with your new profile again. One way (the only way on a Mac?) to do this is to open Thunderbird with your default proflie, then go to Help > Troubleshooting information > about:profiles again.
8. See if the copied mbox files appear in your Local Folders account in your new profile.

I would do all that because, if it worked, I would know that I could still access my saved messages and that the worst case for recovery from this problem may be re-creating my profile and copying files, which is not a terrible thing. I don't know what caused this problem and I don't know how to fix it, but I'm relatively happy if I know how to slither out of it with my messages.

Other people may have other/better ideas.

But we should still try to figure out what caused this problem. On Windows, one always asks about anti-virus software, which is rare on the Mac. Are you using any? Do you know anything else that might interefere with Thunderbird's use of files?

On 07/22/2025 I went to download some messages via my ISP POP account and saw that a whole bunch of my email folders no longer had any subfolders and were empty of any messages. Some were also duplicated.

Matt thinks that this account is not a POP account. The file path indicates Local Folders, not a POP account. But you went on line to get messages. Would you say more about this account in Thunderbird? Does it retrieve messages from a server? Can you send from it in Thunderbird? Do you know why it has an Outbox? Are there unsent messages in the Outbox?

You've cited two macOS versions. Which are you on?

Rick, Thank you for your various thoughts and suggestions. Yes, I HAVE content in my mail files, not sure what to call them in Thunderbird terminology. The issue is that the application no longer understands how to... again, not sure this is the right word, but index the messages. I have some 3Gig worth of email in the local folders, all in a folder hierarchy.

I did a version of what you suggested. - I backed up my ~/User/Library/Thunderbird folder both locally, so I could access it, and on an external removable drive. - While Thunderbird was not active, I deleted ~/User/Library/Thunderbird. - I then started the application again and re-made my POP account. - I then quit Thunderbird. - I then copied in a couple of the mail files into my new ~/User/Library/Thunderbird/Profiles/419p2lrd.default-esr/Mail/Local Folders directory. - I started Thunderbird and those files were now folders in my "Local Folders" with numerous emails in them.

This is great, save for one thing. I have probably several hundred (thousand?) folders and sub-folders from years of organizing my emails. This solution seems to be that I have to have every file be a folder with no hierarchy or organization. Is there any way to get the folders (.sbd?) over as well?

To further explain my email accounts which I have configured in Thunderbird. - I had one POP account with Verison. This is my personal email which I manually manage via the web GUI. When I am ready to 'archive' the email message, I download it to Thunderbird via POP and place in a folder of my choice to safe keeping. - I had a secondary POP account with Version for my family. It is still active but has not been used in then plus years. I made an account in Thunderbird for this but do not use it. - I have a GMail account which I manage via the WebGUI and do not use much. I created this in Thunderbird predominately as a test to see how it worked.

Thus, when I created a new account to test in Thunderbird, I only set up my Verizon POP account. The GMail and other POP account aren't really a thing for me.

Since this problem developed, Apple has released several new OS updates and Thunderbird has also updated the application several times. To solve my issue, it is not necessarily a good idea to update, but my hope was that the updates, at least with Thunderbird, might fix my issues. Thus, the multiple versions of things. At the moment I am current for Apple OS and Thunderbird version for Mac.

This is great, save for one thing. I have probably several hundred (thousand?) folders and sub-folders from years of organizing my emails. This solution seems to be that I have to have every file be a folder with no hierarchy or organization. Is there any way to get the folders (.sbd?) over as well? </blockquote. <p>I thought that copying the whole folder structure should work, but it did not work for me just now.

Would you please state your specific macOS and Thunderbird versions? There are two "current" versions of Thunderbird. "Current" might mean different things to different people right after Apple released a new operating system version, and you have referred to two versions.

Are you using any anti-virus software? Do you know anything else that might interefere with Thunderbird's use of files?

A common troubleshooting step is to run Thunderbird in troubleshooting mode (under the Help menu) and see if a problem persists. I doubt that it would reveal anything in this case because the symptoms are changes in files, and troubleshooting mode will not reverse those changes. But you might try and see if anything else happens that might tell us something.

Hey all. So, I was finally able to "fix" my issue, although I still don't fully know what the deal was.

As far as I can tell, Thunderbird does not like certain characters in the names of folders. Or rather, older versions didn't care, but suddenly a recent version did.

I had used the "*" at the front of many of my folders to make sure they rose to the top of my lists. Lazy version of using numbers. So, I had things like "* House Stuff" and "*Things The Wife Told Me To Do." <g> Those seemed to be the folders that had issues.

So, I took a copy of my ~/Library/Thunderbird/Mail/Local Folders and went through every single folder and changed any name that has a "*" in it to a number "01" or "02", etc. I also deleted any folder or file that had random number for a name. They were all empty. I also found mail files that had some weird numbers in their names. I'm guessing that was due to Thunderbird not understanding the character I had used. I cleaned those up.

I then did a search in this folder for any .msf file and deleted that.

I cleared my ~/Library/Thunderbird/Mail/Local Folders folder and dropped this 'cleaned' mail files and folders in and started Thunderbird.

I now have, I believe, everything back and Thunderbird is working fine.

Moral of the story: don't use "weird" characters in names and keep backups of your email.

Rick, to close out your questions: - Apple OS = 26.0.1 (25A362) - Thunderbird = 140.3.1esr (20250929214837)

And no, I'm not running Anti-Virus. Cocky Apple guy.

Thank you to everyone who responded.