Thunderbird is expunging when configured to only mark for delete.
After a recent upgrade to 45.5.1, Thunderbird now does an EXPUNGE (Compact) without my permission. The server settings show "When I delete a message:" as "Just mark it as deleted", and this is how it has behaved for years. "Clean up ('Expunge') Inbox in Exit" and "Empty Trash on Exit" are NOT checked. Suddenly, when I mark the last message in the folder, or sometimes other messages, it automatically EXPUNGEs. I think this is a bug.
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I have a log of it doing this, red-handed:
110084096[11764f660]: 23b89a00:imap.example.com:S-INBOX:CreateNewLineFromSocket: * 11316 EXPUNGE
I never touched Compact.
I turned off Synchronization and it stopped. So it's in the logic that tries to decide whether to EXPUNGE (the "delete model"), or over some threshold I haven't yet found. I do have 11,000 messages in the inbox of this account.