nrgbod
Our Sony Z5 Premium Dual was also updated to 6.0 MM build 32.1.4.1.163 (from Lollipop) via OTA. We had existing folders that we did not want to delete on the external SD card to keep the testing environment unchanged. The following procedure worked for 1.4 type folders:
uninstall Sync
delete all the .sync folders in each of the directories (won't work otherwise, both LL and MM; and it should solve the problem that you mention)
install beta testing 2.3.5.477
Before creating any synchronizations
> Settings > Advanced
tick simple mode (might not be relevant)
change Default Folder Location to "SD://" (this appears relevant, though we do not know why)
DO NOT ATTEMPT TO SYNC MORE THAN ONE FOLDER AT THE TIME, if they are over 1GB (we found this by trial and error, though the beta version seems to sync the folders sequentially so it should not matter in principle)
for each folder on the External SD Card: DO NOT ACCEPT THE DEFAULT. Change and select an existing folder that you created (again by trial and error, but we ended up with duplicate folders tagged _1 if we did not do this, so better be safe)
Wait a couple of minutes and then you can select undo "Selective Sync"(click on the little "i" icon on the right of the folder) to sync the entire folder. (If the selective sync revert to ON automatically, you may have problems though this no longer happened on the beta version).
REPEAT FOR EACH SUBSEQUENT FOLDER ONCE THE PREVIOUS ONE HAS SYNCED
thereafter, everything should work as normal.
Hope this helps. Good luck
Eric