The "SyncShelves" option was a non-supported option in the firmware. It has been removed in a recent firmware.
For the sync, nothing about the sideloaded books are synced. If you have collections with only sideloaded books, then collection name will be synced, but the it won't have any books on it.
The lines in the config file with the collection names are recording that collections configuration. There could be a line for each collection with the sort, filter and which view you are using. I don't believe this gets synced.
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