Flags in Apple Mail Disappeared

So… I'm happily using Sierra on my 27" iMac (5k 2017), when I decide to install Monterey on an external flash drive to see what it's like. This should, of course, not affect my internal boot drive in any way — right?

But once all that is over & I've restarted from my Sierra drive, I launch Apple Mail & discover that all my hundreds of flagged emails are no longer flagged. Which is REALLY serious as far as I'm concerned, since I have tens of thousands of emails, & only flags to show me the vital ones, most of which are years or even decades old. Needles in a haystack, in fact.

What have I done to try & fix this?

I used Time Machine to restore com.apple.mail.plist in [Me] > Library > Preferences (although that file is tiny, so little hope of success. And also my entire Mail folder in my Library; it's 7.12Gb, so this was no small job. This renamed the existing folder "Mail (original)", which I've moved to a safe location, but both folders are effectively the same anyway — it turns out.

I went back to before the 'install Monterey elsewhere' attempt.

But no success. Is there any way I can get my flags back?

(I should add for full disclosure that two emails did still have the correct flags. But there are hundreds of emails which have lost their flags — & don't know where to find them.)