I was recently affected by the CCleaner glitch which wiped out everything on TB. Fortunately I recovered the emails, but had to reinstall TB. Now after downloading my emails into TB and I go to my server's web site (Xfinity) and delete those emails, the emails in my TB Inbox disappears. If I put them back on the server, they reappear on TB. The only way around this on TB, so far, is to create a new folder and move any emails to that folder. Then if I move emails on the server to Trash, the ones on TB remain. Before the crash, this didn't happen on TB. Emails remained in the Inbox until I deleted them.

I figure I probably need to check or uncheck something in the settings, but don't know what.