The scenario: I have an email account on a server that I also have ssh access to. Normally I check this account via IMAP in Thunderbird (currently 3.0.8 on Ubuntu) and IMAP on my phone (Nexus One, default mail app). Occasionally I use a web interface (Squirrelmail 1.4.20).
Earlier today I used Alpine locally on the mail server to read a message. This was the first time I had ever used Alpine with this account on this server. Afterwards, all of my old mail disappeared from both IMAP clients and the web interface. The mail is not gone; it shows up just fine in Alpine, and it's still in the mbox in my home directory on the server.
However, I cannot figure out how to get it to show up again in any other client. I've tried un- and re- subscribing to folders in Thunderbird as well as creating a new account. I'm assuming Alpine changed something, but I can't see what or how to undo it.
Note: If it wasn't clear, new email (since using Alpine) shows up as expected in Thunderbird, etc.