Jiquani's Machinarium soul cores disappear from inventory, when portaling encampment

In order to decrease the annoyance of running the labyrinth 10 times, I placed a portal on one end, then walked to another, picked up 2 soul cores and entered the waypoint. Then, from encampment, I used the portal I had placed before to enter again into Jiquani's Machinarium. The two cores were now missing from my inventory, and I could not open the doors. I had to start a new instance on the dungeon.

1. portaling back and forth only drops the soul cores on the ground where you left through the portal.

2. not sure why my soul core disappeared that I had before the boss fight, because I haven't been looking for it's absence during the three times I died. But after defeating the boss and going to camp and back, I now have no remaining core anymore.

upd: just found one soul core in place on the map that I have already un-veiled. Not sure if it just respawned or respawned and randomly placed.