To make sure that I understand: When you look at the contents of the all mail folder in Thunderbird (not in the file system), you see many messages, including those that you deleted. Those messages appear normal. Their rows in the message table are not, for example, struck through. There are few messages in the trash folder. When you look at the contents of the all mail folder in webmail at Proton, you see very few messages.

Is all that correct?

Standard actions to try in similar situations are first to make a back-up copy of your profile, then empty the trash (apparently, this step is required to get messages out of the all mail folder even if they have already been "deleted") and see if it makes a difference. Then compact folders and see if it makes a difference.

But if my understanding of your situation is correct, I do not know a reason why those actions would help. Something has caused Thunderbird and Proton to become out of sync. The only thing that I know enough to suspect is the Proton Mail Bridge app. Do you always run it when you use Thunderbird? You have to run it, don't you?

But you could do back-up, empty trash, and compact folders anyway and see if those actions make any difference.

Thanks for your response. The All Mail folder in the main Thunderbird screen only contains a few entries for the inbox and a couple of other folders. Only about a dozen messages. The All Mail folder in the system (appdata) is the one that contains all of the old entries. The Protonmail web version is clean excepting the same dozen messages in Thunderbird. I have compacted all folders with no difference.

And, yes, the Proton Bridge must be used.

I renamed the All Mail folder and the All Mail.msf folder from the profile folder in appdata. When launching Thunderbird again, it deleted the renamed folders, created new ones and populated the two folders properly. However, when deleting messages and emptying the trash, the messages remain in the two All Mail folders mentioned above. They do not appear in the main app folder.

However, when deleting messages and emptying the trash, the messages remain in the two All Mail folders mentioned above. They do not appear in the main app folder.

This is not clear to me.

Are you saying that all the messages that are making the all mail folder big in the file system are actually stored in sub-folders of the all mail folder? And you can see those messages in those folders from within Thunderbird? And they remained in those folders even after you deleted them and emptied the trash?

What is "the main app folder"?

After having rebuilt the two profile folders in question, deleted messages are now removed after performing a folder compact. That did not work before.

Let's just call this resolved.

Thanks so much for your time!