Bug POE2 - Character progression stuck on placing large soul gem in stone altar

I killed the monster holding the large soul gem, then opened up the waterway, but the gem was still in my inventory. I dropped it and completed the waterway, but the lever at the end did not unflood everything, and now I cannot re-activate the stone altar. I have gone back ad killed the monster holding the large soul gem again, but I did not get a replacement gem.