mail emails missing, TimeMachine recovery unsuccessful

Here's my story, with 4 specific questions at the end.

My mail setup is a little complex, but, until today, has worked pretty well.

Currently my 2 gmail accounts collect all the mail from my various addresses.

Mac Mail then uses IMAP to connect (as do my iphone and ipad).

I also have MailTags running.

My normal processing is that once I've read an email, and I want to keep it, I move it to a folder called Done which is on the Mac.

I then used Mail Search capabilities to find what I needed.

I alos used flags and Mailags keywords or projects to make some messages easier to find.

Done should have thousands of emails.

But I noticed yesterday that it had no emails after 22 June this year.

And when I tried searching for emails that I know existed from earlier this year, but Mail couldn't find them. Spotlight found some of them.

I tried recovering from TimeMachine a version from a few days ago when I thought it was all OK.

First I tried recovering juts the 'Done' folder. That didnt work. So then I recovered the complete Mail directory.

(Each time I did this at the file level by copying the folder I wanted from the TimeMachine disk over to the harddisk).

Each time Mail then reindexed. And MailTags rebuilt itself too. So its a slow operation

But to no avail.

Mail is still missing lots of messages. (However, they are still on copies of the files I made before I did any restores. So Spotlight finds them. But they are not in Mail.

Almost none of my flagged emails are there (in fact 3 flags are missing altogether). Most of the keywords are missing.

And folders like Drafts and Outbox have a bizarre collection of emails going back years - 8 in Drafts and 19 in Outbox.

Right now I forced Spotlight to reindex itself but I suspect it wont change much.

1. Is there a way I can force the messages I find back into Mail?

2. Is recovering individual mailboxes realistic, or likely to make matters worse?

3. What does Mail's rebuild option do for mailboxes on the mac ie not Inboxes ?

There's a possibility I did this on my Done folder, and this is part of the problem. I would need to go back a week ago to get before this time (I'm missing a few days of time machine backups )

4. Flags - where are these stored? Will these come back when the mails are back ?