Your mail provider is who? What happens has a lot to do with the provider. Some simply ignore the delete command unless you make changes on their web mail. Others change the ids of the messages after they are downloaded so they don't delete because the message to delete is for the Id. The later however is usually accompanied by everything redownloading.

gmx.com. I set up an XP VM on the same host as my Thunderbird 91.8 and installed Thunderbird 52.9.1 (32 bit) on it. I've had this account for years and had been having no trouble with Thunderbird 52.9 so I tried some experiments.

1. I sent myself an email from the 91 Thunderbird, downloaded it on 91 and deleted it. Then I checked for new mail in 52 and it downloaded the message I had just deleted in 91. But then I checked for new mail in 91 and it said there was nothing there. Checked for new mail in 52 and nothing there.

2. Sent myself a message from 91, downloaded it in 91 and deleted it in 91. Checked for new mail in 91 and it said nothing there, so that's correct. Checked for new mail in 52 and it downloaded the message I'd just deleted in 91. Checked for mail in 91 and it said nothing there. Checked for new mail in 52 and it said nothing there. Went to GMX's web mail interface and the message was still there.

But I refreshed the web UI 10 minutes later and the message I had deleted in Thunderbird was gone. Meanwhile I received four new messages. Downloaded them and deleted them in 91. Checked mail in 52 and the same four messages downloaded there. Checked new mail in both 91 and 52 and it says no new mail. Checked the web UI and all four messages are still there. An hour later they're still there but doing another download says there's no new mail.

So I tentatively conclude that gmx is temporarily confused about message deletion and that this started just as I was switching over from Thunderbird 52 to 91. I'm going to wait a few more days to see if this clears up on its own. (gmx's customer service is useless. They never even reply to questions.)

Some years ago Hotmail was taking up to four hours to delete mail (in their case they moved it to the pop folder and ignored the deletion request. If you were like me deleted on download, the same mail might arrive a dozen times.

Well after observing the behavior of downloaded and deleted messages for a couple of days, it's looking pretty non-deterministic. Some messages get deleted immediately, others stick around a few minutes before disappearing from the server, other a few days. But it's looking like this is in fact a gmx problem, not Thunderbird. You can see how I thought so though since I'd never had this problem until I cut over to the latest version. Thanks for your help.