I don't know if this would be relevant to you but I had this same issue last week, though our problems might be different figured I'd throw my 2 cents in just in case it helps.
What was causing this problem for me is when I connected my phone to my computer my computer wouldn't recognize the device, nothing would show up in the explorer window, after some troubleshooting I switched my phone from a MTP device to a PTP device and suddenly my computer saw the device and let me access it's directories. I was able to sync no problem the first time but adding just 1 more song caused it to re-sync the entire library again, confused as to why it was doing this I opened my phones folders in windows explorer only to find no music files there but when I checked with my phones file manger they were all there. It took longer than I would like to say to find out my computer was showing nothing there because as a PTP device it only displayed picture files even if the music files were there, so when Musicbee went to sync that 1 additional song it saw the music directory was empty and started re-syncing everything again, my quick fix was to use the wifi sync as that bypasses if my computer can see the music files or not and have had no issues syncing since switching to wifi only.
Long story short when you connect your device make sure you can see the music files in windows explorer as if your computer can't see them musicbee can't either and will assume the folder is empty.