I have had that happen a couple of times - don't know why and I can not reproduce it.
A couple of surface items that might come in handy is to use either of the following:
Surface Snapshots: Freezes the surface build to that point. Useless if you change anything under that snapshot during editting but if a feature line disappears, the data was captured in the snapshot.
Copy Dependent data - this is a surface setting that will copy surface data into a surface definition if removed from the drawing.
Matthew Anderson, PE
Joseph A Schudt & Associates
Matthew Anderson, PE CFM
Product Manager
Autodesk (Innovyze)