I've had that happen a few times to me and a couple of my customers.
Every time it seems to have been a glitch with an IMAP server (never POP).
PIPEX seemed to be especially prone to it a couple of years ago. It was damned disturbing when a few hundred messages I thought were safely deleted suddenly downloaded again
My guess would be a broken server thats been partially restored from a backup.
Were you using IMAP mail?