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I suspect that with the introduction of JMAP in the backend, the way messages are stored and managed may have changed in a way that effects deletion of individual messages. I would suggest a support request, asking about the behaviour change, and asking if there is a clean way of keeping the message in one folder while removing the same message from a different folder.
The only circumvention I can think of for now is to move the message back from Deleted Items to the desired folder after the delete. Possibly, rather than deleting the message, it may be possible to move it from the folder it is no longer wanted to Deleted Items. You could try it to see what happens.
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