I faced with the following issue in the Precipice.
I defeated void touched worm idol and the time rift to Ancient Era was opened and the new quest “An Ancient Path” was added to the journal. At first I used town portal to move to refuge to clear (sell) my inventory and to craft. Once I returned the rift disappeared but the quest was still active:
Since the Idol didn’t appear I had to run new game session and it worked - one more fight with the worm and the rift was opened again.
P.S: If you use town portal after completing quest from Last Imperial and you don’t loot the chests you will lose it, i.e. chests will disappear and that’s all.