It is awful quiet around this question.
Nobody knows without restoring them all.?
Once I found this - does this work? -It is from 6 years ago
The hidden command x-remove-dups removes all emails with duplicate message-ids. Please note that this may be dangerous as message ids are sometimes not as unique as they should be.
the command you refer to is not available in the current MSH. And there is no "remove duplicates function" in MSH that you can trigger across the archive.
Removing emails in the archive can only be done manually. If you see similar emails then look up the header UID ́s. Such emails may have different origins (e.g. imported from two sources, two PST and so on).
If such emails originate from different sources they are not considered duplicate (though they might be similar).
Check email headers and compare the UID ́s (1, 2 and sometimes 3) AND the origin of such email.
Example of "apprently" duplicate but only similar emails. Top email first:
Second email is similar, but since the UID values (blue arrows) differ due to the source of import they are not the duplicate.
As a note: I actually moved one email out and reimported it - then moved both emails into the same MSH folder location "Test" that is blurred out on the screens.