I've seen this three times already, though it's not easy to reproduce. I have a few IMAP accounts with many folders and periodic mail checks enabled. It happens that when I edit a message in the foreground, claws starts checking mail in the background and I click 'send'. Now, usually that works somehow. However, there's some hidden ugly race condition that sometimes makes claws confuse 'Queue' with another folder. Long story short, claws hangs for a while (fetching mail bodies, I guess) and then suddenly 'Queue' contains 1000+ mails that were really in another folder.
The other race I noted is that the filtering rules are not run on received messages.
are messages really moved or is it just the cache file that gets messed up?
Just the cache.