OSX 10.9.5 Mail: Flagged messages not listed correctly and/or disappearing

I have a problem using Mail V7.3(1878.6) on OSX 10.9.5:
I have about 600 flagged E-Mails in various account inboxes and archived folders, some archives are stored local on the mac, others are archived in folders on IMAP servers (NOT gmail). Total number of mail messages across all accounts is approx. 34.000.
Since the 10.9.5 update, Mail shows no flagged messages anymore or behaves weirdly. If I flag a new message, it shows up but disappears again after a while, e.g. a restart. Searching for flagged messages shows no results, even though I can see hundreds of flags in my inbox behind the messages.
I have rebuilt the mailboxes and also rebuilt the index by removing the "Envelope.*" files in user/library/mail/v2/maildata as suggested in other threads a number of times, but nothing seems to change. After each Envelope rebuild, Mail shows flags again (sometimes the correct, sometimes the wrong number, only 100 odd) and after a while they disappear again. Making a simple smart mailbox with "mail is flagged" as the only option, the smart mailbox remains empty. This has never happened before 10.9.5.
I would appreciate a comment as to what is happening here. Seems this affects quite a few people based on the activity on this subject here and in various other Mac forums on the net, but no other solution has yet been given than rebuilding indexes, which obviously leads to no permanent fix.
Thanks.

Restart the computer in safe mode. Certain caches maintained by the system will be rebuilt.
Safe mode is much slower to start up than normal. The next normal startup may also be somewhat slow.
When the login screen appears, restart as usual (not in safe mode) and test. There's no need to log in while in safe mode.
Note: If FileVault is enabled, or if a firmware password is set, or if the startup volume is a software RAID, you can’t start in safe mode. In that case, ask for instructions.

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OSX 10.9.5 Mail: Flagged messages not listed correctly and/or disappearing

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