Bad rules mangled my mail: how to fix?

I set up rules badly for my Mail. I had several sets of rules where *any* of two rules had to be met and then the mail was put in one mailbox or another. It turns out that all my mail met a couple of the rules!
So I started noticing a LOT of mail in these mailboxes.
Then I deleted some of the rules and moved the contents of the mailboxes back into the Inbox. Then I re-wrote the rules correctly so that only if *all* conditions were met would the mail go into one box or another. But I still had a couple mal-formed rules with the *any* option selected.
I decided to delete ALL my rules and to move all the mail from those boxes back into the Inbox.
Somewhere in the middle of doing this I noticed that recently received mail was mis-displaying. An email would have a header from one person but the body of another email! YIKES! Then search started acting up.
Also while I was doing this I was hearing Mail crunching along in the background.
I had a lot of mail accidentally put into those wrong mailboxes. So in the end, after those several partial changes, I patiently waited for all 25k emails to transfer back into my Inbox. Then I quit Mail and restarted it. It now SEEMS like some of the mal-formed mail is GRADUALLY getting better.
Is there some kind of re-indexing I should make Mail do to really fix things?
I once tried Rebuild and got into BIG trouble. (A lesson there that I vaguely recall is that you have to let it finish without interruption. I had thought that it had stalled and force-quit Mail in the middle of Rebuild.)
Or will Mail gradually re-index itself and self-recover from my mangle-ations?
I see official info on how to re-index, but don't want to do anything until I get my bearings.
Thanks!

RE-INDEXING WORKED!
Mailboxes intact, etc.
Garbled emails are fixed.

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