Only title and artist are important and if you set them you will never see a song with a filename as the title (well except if you set the filename as the title in the tag).
And regarding song deletion: When there are multiple songs pointing to an audio file, The file will not be deleted when deleting a song. When the audio file is used by only one song, you can specify whether to keep or delete the file.
Regarding the sync problems: The next version will add detailed logging to logfile. I hope I will be able to figure out what is going wrong on your devices when I see the log file.