Lost all crafted items after leaving Realm

Mostly done with Sylvan's Realm, I crafted a crude portal to finish that questline. Somewhere I managed to pick up the desert biome card. I traveled there, completed a couple POIs, filled my inventory, then teleported back to the Crossroads. Traveling back to Sylvan's Cradle has completely refreshed the realm. All trees and ore deposits are back, all my crafted structures are gone, all my items are gone, the POIs are reset, and Aurelio is also gone. I had already completed to storyline all the way to "Find the Heart", and now it seems like I have to partially start all over.