Replying to my own message...the version of Thunderbird is 128.3.1esr (64-bit).

Try disabling your antivirus and see if that make any significant change? Deleting means Thunderbird will open the store file, mark the email deleted, close it, open it and read the message list again. Opens and closes have been made more frequent in an attempt to make data more resilient.

I think what could be happening is there is a scan happening after you take an action and Thunderbird can not gain access to the necessary data.

if the disabling of the antivirus shows promise, try adding the Thunderbird profile to the antivirus as an exception and see if that offers a long term result.

Another possibility is the profile itself is unavailable because the location it is stored on is being syncronised to some cloud location. I notice folk trying to place their profiles into cloud sync rather unsuccessfully more and more. Or placing it in documents and trying to have the Windows back it up to the cloud. Have you moved the Thunderbird profile from it's default location?

Thank you for the suggestions Matt, much appreciated, especially the description of what "delete" actually means. Going forward I'll pay attention to the activity indicator and avoid the delete function if something else is going on at the same time.

I'm not using antivirus except on-demand, so that should not be the cause. The Thunderbird profiles reside safely out of harms way deep within the snap folder.

Following up yet again, the problem is less frequent as of Thunderbird 128.4.0esr (64-bit), but still happens occasionally.