Not able to get completion rewards

My friend and I were playing and had just cleared the Welkins reachstory realm. We returned to crossways and I had to leave, so I left my game open for him to finish up what he was doing.
When I came back the next time, I went to Magwytch marshes for the first time, but he must have gone there first. The town area was liberated and one of the quests must have been done because the turn in was available, but other things like infestation are completed but there is no essence bundle to collect.
Unable to reset the realm either as some message is displayed about needing a biome card, but the crossroads portals don't work that way.