Can we just check that you are never exporting from the sub-realm and importing back into the main realm?
No. What happened is that i created a Realm called "5e Mechanics" where i put all the spells, Conditions, equipment, feats, etc... to be umported into new content realms, so that i don't have to keep doing it over and over when i start a new campaign. That's what i'm importing.
WELL. After all that here is what i did.
1) Reset my main realm to the backup i had just before the import that jacked everything up.
2) Synced everything, which took forever because i had to do them one at a time (Actually, i got sick of this so i deleted Isle of Kandril, Goblins, and the pixie thing to shorten it).
3) Immediately did a full realm export once i verified that everything was where it was supposed to be with the restore.
4) Created a new realm.
5) Imported the full realm export into the new realm.
6) Imported "5e Mechanics" into the new realm.
7) Practically fell out of my chair because it started actually working.
Now everything looks right. I'm still poking around. I plan to sync everything a few times and make sure RW isn't still acting screwy. Probably bust out my laptop and sync everything there as well. But for now it looks like it's acting right.