This may have several issues. What appears to be happening is that the file with your settings (prefs.js) is being prevented from being updated when Thunderbird shuts down. That may be because the file is read-only, or you may be using an antivirus that interrupts the save process. You can investigate this by clicking help>troubleshootinginformation, scroll to 'profile folder' and click 'open folder' and then exit thunderbird. You will be in the profile now. If you see multiple prefs files (such as prefs-1.js, prefs-2.js, etc) that indicates that thunderbird is trying to save but unable to. If there is just one prefs.js, then rightclick and see if it is read-only. If there are multiple prefs files, delete all except the one with highest number, and rename it to prefs.js and restart thunderbird. if you cannot rename because the file already exists, then you will need to click in windows file explorer 'view' menu to show hidden items so you can delete the existing prefs.js. Other than this, I do not know what is causing the problem for you.

Reset Unified Folders: https://support.mozilla.org/en-US/questions/1429758

@david thanks for the lengthy reply and trying to help! I went through the steps you provided, but my client only creates a single prefs.js file (named just like that without a number before the file extension). This single file is also not in read-only mode as indicated by the file's properties in Windows.

@sfhowes thank you as well for your reply! Sadly following the steps of deleting "virtualFolders.dat" and the "smart mailboxes" folder did not resolve my issue. After starting Thunderbird the "Sent" and "Drafts" folders are not part of their respective unified folders anymore (Simply opening "Properties" and hitting "Update" doesn't add them. Also the window that opens indicates that 4 folders are chosen), but after manually selecting them I am once again back to the old behavior described in my initial comment (after restarting the prompt says 5 folders are part of this search and hitting update adds the folder again without having to manually select it).

This may be account-specific. Thunderbird attempts to locate folder names that are exact matches to folders in other accounts. For some reason, it is not seeing the sent folder as identical to others. I would check the account online to see how the email provider names the folder and also rightclick the folder in thunderbird to see how it is allocated. Otherwise, I have no suggestions.

Hmm but theoretically I could assign any folder to be a part of any unified folder, if I understand correctly? So I do not need to rely on Thunderbird automatically doing that selection for me. A while back I manually assigned all my other email accounts, where some "Templates" and "Trash" folders were not assigned to their respective unified folders automatically. After manually assigning them they are not excluded when restarting the program. All other folders from the problematic account also stay in their unified folder after they were automatically assigned or I assigned them manually ("Inbox" for example was automatically assigned, "Trash" I had to manually assign iirc).

Unified folders must meet specific requirements. For example, I have some folders that are unique to various accounts and those are not listed under unified, but separately under the account names.

> Unified folders must meet specific requirements.

for the automatic assignment to work, but manually I could theoretically add any folder to any unified folder as far as I understand. I wouldn't make much sense to assign an "Inbox" folder to a "Sent" unified folder, but I could do that.

To avoid issues with Unified Folders or to apply more options, try a Saved Search (under File/New...). Choose specific folders and search criteria.

I'm on 144.0.1 and "Saved Search" is not available in the "Find" menu anymore. It got moved to the "Edit > Find" as far as I'm aware.

Regardless, I don't see how this is going to help with my current issue :(

It's under File, not Find (see picture). If the issue is with disappearing folders in Unified, a saved search might be the remedy.

Not for me. I am only able to save a search to a folder via Ctrl + Shift + F or "Edit > Find > Search Messages ..."

While that is a possible workaround, it's sadly not really an elegant solution to what appears to be a bug in Thunderbird :/

PS: What version of Thunderbird are you on? I did some digging a while back when I wanted to add all my "Starred" and "Important" folders to a saved search and encountered other people with the same discrepancies in regards to how to add a saved search.

The Saved Search menu item doesn't appear when the current folder is a unified folder. Select a regular account Inbox. If Starred and Important are subscribed folders, they can be added to a saved search. Or, to create a saved search that collects all starred messages in multiple folders, see the attached picture.

Aaah that makes sense now. I didn't know that you had to select a regular folder before, as I only work in the unified folders panel.

So the strangest thing just happened: I was playing around with saved searches and for some reason Thunderbird now remembers my manual allocation of the two folders to their respective unified folders? I am not sure what happened to be honest and at this point I'm too afraid to ask as it might upset the Thunderbird gods lol