I noticed on the wifi sync that one file keeps deleting/copying over and over again, even if I had just synced it. Right now it's the ONLY one, everything else is fine. I tested with a wired sync and got the same result. The date for last modified is 4-12-19.
I use "preserve folders and filenames" and just made some changes to my organization templates, so perhaps that's related. But I have plenty of other tracks with similar album/track names, so I'm not sure why this one would be different.
I have the same/a similar issue, but instead of a song that keeps syncing, it's a playlist. A week or so ago when I was testing for the "preserve folders and filenames" bug, I enabled the "preserve" option, changed the sync folder to a different one so it wouldn't interfere with my library, and then synced a Test.m3u playlist with a few tracks.
After my tests, I reverted the settings back to what I normally use and MusicBee deleted what isn't in the sync profile. To this day, I briefly see "Deleting Music/Unrated.m3u" (I later tested again with this playlist) for each sync, although that playlist doesn't exist on my phone or sync profile anymore. This doesn't break anything, though.
Even on the latest version of the app and the MusicBee patch from above, it doesn't appear in the error logs.