Q: How to sync directory changes

Are you talking about the quick upload feature? (http://www.textasticapp.com/manual/lessons/How_can_I_quickly_upload_downloaded_files.html)

If the directory structure changes, you can just use the regular file transfer screen (using the "globe" button) and transfer your files there. The remote file view will reflect the current directory structure on the remote server.

You can also manually move local folders (see http://www.textasticapp.com/manual/lessons/How_can_I_move__copy_and_rename_files_and_folders.html). If there were extensive directory structure changes on the server, you can also just re-download the necessary folders (possible overwriting local changes).

It's the possibility of overwriting local changes that causes me pain.