You need to parent the skullcap to the head and then save it  to the library.

Deleting just the skullcap is normal behavior for what is a group of parented props. There are some python scripts that will delete the entire group.

The parent universe only says that the prop is unparented when loaded, a setparent should work.

I would check the parenting in the hierarchy editor. If that appears correct you may have a bug.

what version of Poser ?