I'll add my 2 cents worth since I am having a similar problem with variations on the theme.
When I upgraded to Mavericks, the Apple mail worked fine as it has for years. I think that the problem started when I upgraded to 10.9.1. I also use a PC for much of my email (Gmail), but the same Gmail accounts are tied to both the iMac and the PC, so whatever is done on the PC for deletions, additions, subfolders, etc. is also mirrored on the Mac Mail. On the iMac email account, I have the primary account Inbox for lableled "HH-Gmail". Under this, I have about 50 subfolders into which I move my emails after reading and completing any activity associated with the particular email. So, at any one time, I may only have a few emails in the HH-Gmail box with everything else stored in the specific subfolders. Normally, I have about 800 emails, only 7 of these in the HH-Gmail inbox, with the rest in the appropriate folders.
When I came back to the iMac a few days ago, I found the following:
All emails were correctly seen amd could be accessed in folders:
HH-Gmail Inbox/Sent/Trash/All Mail
All of the subfolder contents were gone completely. (This was not the case for the PC, since here, nothing had changed and nothing was lost.)
I have tried most of the remedies suggested in this thread which included a complete uninstall and reinstall of the account with no success. I even tried to send myself an email which could be applied to the specific subfoldeer and has it remained for over 24 hours without being deleted from its subfolder.
One interesting fact is this: one can right click on any folder or go to the menu bar Mail/Window and click on the "Account Info" to see what is in the entire account. If I do this as soon as I open Mail, it shows the complete list of folders and subfolders listing the number of messages and size. In my case, every email shows up in its respective folder and at the end of the list, it shows 800 messages, which is what I should be able to see in the email account. It also shows in MB and GB what is currently in use and the total available.
Now, if I click on one of the subfolders in Mail, which shows all emails deleted, and I watch the Account Info list, that particular subfolder will change from its present number of messages to a zero, which is reflecting what it is seeing in the present Apple Mail account.
Obviously, this shows that nothing has changed as far as the Gmail account, itself, is concerned since everything has stayed constant on the PC AND everything shows correctly on the iMac Account Info listing. Somehow, there is a disconnect between the Apple Mail and the Gmail which cannot be corrected using any of the techniques suggested so far. I am surprised that it takes a fair amount of time for the Account Info to update between the time I click on a specific empty folder and the time it registers zero on the Account Info listing. In fact, it is even more surprising that the Account Info listing requires this action before it will even change to zero. So, the Account Info does not seem to interact even though the Apple Mail has been opened, but not used. Even with the complexity that may exist in finding the problem, I find it difficult to believe that with all of the talent at Apple, so much time has transpired without a fix.
I don't know if any of this will be of help to anyone, but perhaps, it may suggest something to someone.