May be a Trash options problem
On the troublesome installation, look at the "Mailboxes" list on the left-hand side. You might have to go View > Show Mailbox List to see it.
Is there a triangle to the left of the Trash mailbox? If there is, click it and expand the Trash mailbox. Which mailbox do the deleted messages re-appear in?
If they're appearing in "On My Mac" or similar then I would guess the Trash options need a look. Go to Mail > Preferences > Accounts. Highlight the Account on the left and look at the Mailbox Behaviors tab. Both the Trash options need to be ticked for deleted messages to end up in the right place, but Mail does have a feature of options not sticking so untick them, quit, restart, tick, quit, do this two-three times leaving them ultimately ticked.
Let us know if that makes any difference.
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