I am sort of a rooky but I will try to help.

I have had the same problem but have never had to regenerate the model in SE.

The diminsion with a line under it means it is in conflict another diminsion.

Right click and edit the part. then edit the profile and see if another diminsion is holding it there. Also click edit definition and see it there is a diminsion there holding it where it is.

Sounds like you made that protrusion on a different plane. (maybe)

This could be all wrong but it is what I would try.