I am completely unsure how this happened. I had just finished a realm in Azural’s frozen realm of depth 65 instability 5. I had also just finished a training mission for attack scrolls. All the spell gems my creatures had equipped are now just gone. They were all chaos gems of mixed levels as I was in the process of gathering resources to power them up. I can provide a save file if it might help.
Spell gems that were in my inventory appear to be unaffected.