Will collagen, gelatine and mineral nutrients be lost when fat is removed from broth?
Most of what you're interested is in the water/broth, not the fat.

This is especially obvious for the gelatin; the whole reason that broth has that nice mouthfeel and thickens or gels when chilled is that it's full of gelatin. The other proteins and nutrients are just as water-soluble.

You may end up with some particles mixed into the fat, so it might not be pure fat, but it's pretty close.