I started the orowyrm fight and grabbed the orvius, then I saw that the owl side quest was still available. I started it because I wanted to see what would happen, and it seems that it removed the orvius from me, and it was no longer available at the fast travel point I started the fight at, which softlocked me. I tried swapping weapons to see if that would somehow give me the orvius, but that didn't work.
This is the image of me being unarmed with the orowyrm present:
This is the image of the owl side quest during the orowyrm fight:
I do not know if this happens with the other optional quests.