This means that you or shared users whom you gave the ‘Sync’ privilege, have created Sync jobs which are not completely downloaded to the target device.
Very often this could be caused by
- old app IDs, which are actually not in use anymore
- user has created sync jobs for whole libraries, or tv shows, or music artists (often unconsciously) which were then subsequently halted, because the target device ran out of space
Old sync jobs which were created for devices which are no longer in use (e.g. the old or lost smart phone), get only cleared out automatically with extreme delay (several months).
Who is responsible and for which apps the Sync job was created, you can see only with Tautulli, atm. It has a separate section called Synced Items.
Only sync jobs where the ‘Downloaded’ column has a lower count than the ‘Converted’ column are actually taking up space on the server.
The screenshot below shows actually only sync jobs which are not taking up space on the server, because they are all download completely to the devices. (100% complete)
Only the user who created the sync job can clear it out again.
If the target device is no longer available, use the web app.
Settings - Status - Sync
Or use Tautulli. 
(‘Delete Mode’)
For backup purposes, I’d simply exempt the whole Transcode folder from the backup
