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0e1f616
(Get the code!)
The bug still lives in 2.28.1.
I found that it should be related with filtering somehow.
In my mailbox settings I turned off 'Apply filters to new messages in Inbox on this server', deleted the folders as described above, and after the next synchronization I can see all of the missing messages.
I have no local mail filters set up, but when this box was checked, I can see my messages while the filtering process was running, but they disappeared immediately when this process finished, but still counted as unread in Inbox.