You can get a medium soul core after you defeated the Zicoatl - Bug Report ID: #3911444205

In Jiquani's sanctum: I have used the two medium soul cores on the generators and defeated zicoatl and got the large soul core. After that I died while exploring the area a bit more and the area reset. I could now once again pick up a medium soul core. So now I have a large and a medium soul core in my inventory.

Here to say: have a friend or someone from discord who is *done and gone* with Act 3, they can come back and get medium soul cores and spawn the boss again to continue. Just unbricked my character with this. Had the same bug, lost my instance with the Large Soul core on the ground and had to find a way to respawn the boss.