As this has caused me some grief and the solution is less than obvious I thought I'd put a brief note here so Google can pick it up.

The issue is that Thunderbird 3.x has a new archive feature which you can't turn off. It allows you to archive a highlighted email by pressing a single key, which appears to default to "A". When you press "A" the highlighted email is moved to a folder "Archives/YYYY" where YYYY is the current year.

Now the problem with this, and you'll see people complaining about it all over the Web so it's not just me, is that if you don't use this feature but you accidentally press "A" your email disappears and you're left scratching your head wondering where it went.

There is a solution however and it comes in two parts:

1. Install the add on Message Archive Options and then in the preferences for the add on set Granuality (sic) to "Single Folder". This removes the "YYYY" feature, so when you press "A" mail is now moved to the folder "Archives". Also check one of the Key Modifiers for Archive Option: 'A' +
2. Go to "Edit|Preferences" and in "Advanced" under the "General" tab click on "Config Editor..." and search for "archive_folder" using the filter. You should find you get one or more entries for "mail.identity.idN.archive_folder" with N being a number starting with 1. Modify each of them to remove the "/Archives" from the end of the string value.

The consequence of the above is that you haven't actually disabled the archives feature, instead you've told Thunderbird that you have to do something you're rather less likely to press than "A" on its own but if you do manage to press "Ctrl-A" or whatever modifier you selected it should archive the email ... back to your inbox. So essentially it becomes a no-op most of the time and at worst it at least moves it to a folder where you're likely to find it.

It's a horrible cludge, but it does seem to work.