Lost mail body and marked messages - Maverick Upgrade

I lost some message body (they are listed but have no content) and 15 out of 16 messages marked with a flag where not in the Marked Message Folder. That happened after upgrading to Maverick. I tried to replace only the Mail folder in the libraray with the old one from Time Capsule. Didn't work. Had to reinstall whole system.

i had lost mail body, this is how i fixed it:
hold option, click GO in the top bar (where the apple icon lives), go to library > Mail > V2
now here's where things may differ slightly, i lost the body of mails i had moved to my computer (on my mac), plus i'm using Gmail accounts, that being said, inside the mailboxes folder is where the local folders are and Mail decided to create duplicate folders of some of them so i had
Clients.mbox (with some emails)
Clients-2.mbox (with the missing ones)
i then moved the Clients-2.mbox to the desktop, went File > Import (in Mail) then selected Apple mail as the import type, selected the mbox folder on the desktop and imported them into mail at which stage i just moved them back in to the clients folder where they belong.
i still have an issue where the reply arrow (next to email subjects of replied emails) is linking to completely irrelevant emails, that is not good. unless apple fixes it asap i would recommend moving to another email program as the Mail dev team has not only dropped the ball but stabbed it repeatedly with a blunt rusty object.

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