10.9.1 update erases contents of IMAP mailboxes (but not Gmail's)

I run a pretty clean system and don't fuss with moving things around and adding 'helper' apps that modify how the system works. (I don't tinker much)
Before applying the update I backed up and repaired permissions.
Applied the update. Everything went smoothly.
Started up Mail, and in my INBOX, all of my IMAP boxes were empty (except Gmail's).
So, I checked my Mail folder in my Library, and indeed the folders for my IMAP inboxes were empty.
I attempted to rebuild the mailboxes, nothing returned.
Fortunately I backed up, BUT...
This action seems quite odd to me and I wanted to report it in case anyoe had a similar problem.

I suspect this problem is not with Gmail or changes Gmail has made recently:
I have 2 loaded iMacs, 2 Mac Airs,and a Macbook Pro with Retina, and 2 iPads, and an iPhone.
I have confirmed on all my iPad and iPhone devices that all my Gmail content is visible, and installing Thunderbird on the iMacs and MacBooks accesses Gmail and the sub-directories.
However, MAIL on the iMacs and MacBooks fails to access the Gmail sub-directory contents dated pre-OSX installation. I have kept everything updated.
PERHAPS NEW INFO TO THIS THREAD: Also, current Time Machine backups fail to show Gmail IMAP sub-directory contents dated pre-OSX installation as well, so this problem appears to be OSX UNIVERSAL not just affecting MAIL. (on one iMac, Mavericks trashed my Time Machine drive (Pegasus - but the company responded quickly with a fix but I lost all the backups). My other iMac (I have one at home, another at work) has a pre-OSX Time Machine backup still that Mavericks has not yet trashed (although it has tried in various ways). The pre-OSX backups show all my Gmail messages in all directories... but post-OSX install the directories show as empty.
Performing a 'Get Account Info' via MAIL 'sometimes' shows a correct Gmail sub-diertory message count, 'sometimes' does not, and 'sometimes fails to report the even the sub-directory name or stats. BUT, doing Show Messages, even whent the message count shows correct, displays an empty directory, or only those messages post-OSX install.
As someone posted earlier, go to 'MAIL' and select 'Provide Feedback' and bombard Apple Support with a bug report.
PS. Thunderbird will not install an iCloud account in IMAP for me, even a manual config from settings in MAIL don't work, and Thunderbird won't 'Import Settings' or 'accounts' or 'folders' or 'Local mail' from MAIL under Mavericks either it seems... reports Info Not Found.
PSS. installing an iCloud account did nothing useful to these problems, and in fact I had to go online into iCloud via the web to create a subdirectory before MAIL or even the iPads etc would see more than the iCloud Inbox.
PSSS. to get MAIL to refresh the Gmail Inbox, I have to shutdown MAIL and re-open it (and sometimes, MAIL takes a long time to shutdown as well).

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I have the same problem. The recent Mavericks update fixed the original Gmail problem (of not being able to get rid of mail from the in box), but this problem is there and very frustrating. Exactly the same as the original post - Mail on my Mac does not reflect the emails filed, moved, deleted etc from my iPad or iPhone. Gmail, iPad and iPhone are all in perfect sync, but the Mac is not.
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I have been looking at alternative mail clients as I have now lost all faith in Apple Mail. (I am committed to IMAP and Gmail, on 3 different email accounts).
Yersterday I tried Outlook (as I happen to have a copy with Office-2011 for Mac). I liked it apart from the fact that it won't work with iCloud contacts... so its no good for me.
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