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As you write, it does appear to be gone.
By default, Fastmail will suppress duplicates within a folder on delivery. I appreciate that this is not the same functionality. I believe the ability to find duplicates ought to be available within advanced search (but it is not). I cannot find any way of doing this through the Fastmail interface now.
If you really need to do a dedup, you will need to do it from a client. Thunderbird has this functionality. If you have no other use for a mail client, there is a Python tool that can do it. That would probably be my choice.
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