So I am constantly getting this message after I make a change to my model and I am forever rolling back my design to try and fix it. My question is, if the problem feature is still there like it was before I removed it's reference geometry and I am able to render it okay, why does it insist on relying on geometry that is no longer there? Can't it just make a new reference to somewhere in 3D space?
You've removed the geometry, but the relations/mates you set up are still there.
It'll keep telling you this until you go in and delete the offending relations (the murky green ones).