In fact I realize that if I refresh references on the ES3ReferenceManager, the current scene .unity file and same 2 prefabs get modified so that the faulty
line gets added in each of those at least once. Is there anything about SpriteAtlas type objects that I should know? Should I just skip adding those types to the references dictionaries?
I've just checked the line numbers for the error message you were getting earlier and it doesn't seem to match up with the current version. If you've already tried updating from the Asset Store, would you be able to send me your invoice number so I can check that you're indeed on the latest version? We've had cases in the past where the Asset Store hasn't been distributing the latest version.
Once we've done this, would you be able to PM me over the complete error message you're getting so I can test to see if there's an edge case we've not accounted for?
It sounds like Unity might create a new instance of these at build time, invalidating any reference to them. Usually Unity flags these as Editor only so that serialisers don't try to reference them, but it sounds like this might not be happening.