I have no idea what you think compact is, but it has nothing to do with deleting mail or moving anything to a new folder, let alone Trash.

Did the copy in Local folders ever contain the email is was it always just a hollow pointer to an empty email.

You say local folders, but do you mean a folder the Local folders account or just a folder in Thunderbird say in an IMAP account..

the local folders were empty, and the folders in Trash contained the missing e-mails. There are no corresponding folders in the e-mail account that IMAP uses. I have NO idea why these emails and folders were transferred to trash but it has happened three times now, and it is a pain to move all back from trash to their original folders.

Any pop accounts? In Account Settings > Server Settings > what is the folder specified for trash? In Account Settings > Copies ...> what is the folder specified for archives?

I just turned off the keep messages in archives - I had a bunch of empty folders in Archives (two of which I could not delete). It had been set to keep messages in All Mail. When I delete a message, move it to trash in my account. I do not delete trash upon exit. I also never use archives, so I am wondering how those folders (most of which were in Trash) were there; however they were empty. I do not use POP but IMAP and download e-mail messages from a google account.