Windows can restore old copies of files, especisally if it decides it has corrupted the current version. Look for windows replacing prefs.js

Thanks for your reply Matt, I removed the account, took a screenshot of the file prefs.js attributes and then restarted the application, the IMAP folder had returned so I went back and checked the file attributes again against the screenshot and there was no change. There are 8 accounts, a mixture of POP and IMAP but this is the only one I have had trouble with and it's always after the second application restart.

that file is read on startup and written at close down of the application. There are some reads and writes in the middle. But your test need to be immediately after closing.

As all of the preferences for everything Thunderbird are stored there, and the data is missing after the first restart (no account) it is clearly being written. That this information reappears after you have proof that the file has been saved only leaves the operating system.

I don't have any idea what. But as Thunderbird does not store a backup of the prefs.js file it can not retrieve the information. Something external has to be involved.