Thank you kindly for your reply, and for checking those suggestions.
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Re: "The only thing I had done was to flag the original email".
Have you tried re-opening that flagged email ... unlikely, yet worth checking there ... (ie: "conversations" may be collected in the one file, depending on settings)
and
check the "Bin" and "Archive" folders (one set for deleted mail)
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Re: " ... it was very annoying that it was deleted outside my control."
Commiserations! Suddenly losing our work is a shock.
Interference from unnecessary third-party (non-Apple) software like ad-blockers, virus-checkers, cleaners and the like, even VPN (if not supplied by an employer) has been found to cause grief in the Mail app by others. Even if turned off, they may keep running in the background. Getting rid of them completely by using un-installers from their developers also deletes their associated files.
( More info: Apple support's info. )
Any third-party apps that you find necessary also need to be kept up-to-date to avoid compatibility issues.
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Else: if you can rule out "third-party" possibilities:
You may want to send feedback to reach those who work on the software behind-the-scenes at Apple. Although they will likely not reply, and it won't help immediately, if others also have a similar issue Apple may address it in a future update. (All feedback is carefully read and logged.)
Web-form for feedback: Feedback - Mail - Apple