I've quoted for an initial review and report of your current problem, which is at a standard fee of $50 and would make a report based on your problems, As a company we specialise in 'common internet technologies' such as mail transfer and migration services, we've done work such as migration from local mailboxes (pc/mac based) to server-based local IMAP as well as other protocol enhancements for local and wide networks, The reason I say this is because we've got extensive experience with mailbox conversion, which would seem a logical solution to your problem (export mailbox which would fix it, then re-download mails possibly) but this would need to have an initial review of the project and until this is done I would not feel confident in giving you an accurate quote on the problem.
We could also if you require this provide possible alternate solutions to stop such problems occuring in the future, using alternate technologies.