That has been my experience, also Demo...happens on my iPhone and iPad, but I have not paid attention to the dating. My experience has been that almost everytime I do a large amount of deleting, maybe need to note just how many or how many are left and see if there is a correlation, I get some "empty" emails appearing that I cannot delete. When that happens, I quit Mail, and then when I reopen Mail there is a full complement of emails present. Emails have been pulled in from those not being displayed due to the limit on number displayed that I am using.
My experience may not be the generic answer...it is the way this has been working for me, so whatever that is worth.
I haven't gone through the process you describe of reset, since the quit/restart has worked.
Obviously this is an "undcoumented feature" of Mail 😝
Do you know if anyone has filed a bug report with Apple on this? Seems like an appropriate thing to do under the circumstances.