When I right click a folder and choose either Sync Remote to Local and Sync Local to Remote, this happens:
Delete remote path "site.org/public/wp/wp-trackback.php"
Delete remote path "site.org/public/wp/xmlrpc.php"
(Select via quick panel) No
I never selected no.
Sometimes the quickpanel would should up asking to choose yes or no, but most of the time it just defaults to No. It's EXTREMELY infuriating to the point where I'm just using Notepad++ until this issue is resolved.