I have 2 stacks of Refined magical black stones and am unable to use the largest stack.

I think the one stack was in the extended inventory when the value pack buff dropped off.

How do I fix this?

Hi there, please try to deposit both stacks in the storage.
You can deposit the stack that is in the "normal" part of the inventory as usual, and then manually move the other stack to an unlocked slot in your inventory before also depositing it in the storage

That worked! Thank you!