Still trying to figure out the best way, but I found a bug in the current shelf system. If you create a shelf and assign only sideloaded books, then when it syncs to BN's systems, it will delete the shelf (not the books, but just the shelf). Although it may only do that when synced to another device or BN app.
Here's what I did:
1) Create shelf and assign only sideloaded books on Nook GL Plus 4
2) Sync
3) From ipad with BN app, sync.
4) Back on Nook, shelves with only sideloaded book assigned are deleted.
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