What Lew says, plus
Are the interferences a very small volume?
Any consistent observations about their positions?
Are any actual dimensions changed?
I use Dynamic motion. Therefore I suppress (but never remove) redundant constraints before transfer to motion. In fact I have a configuration with all constraints applied and a configuration with them suppressed. You could anchor them in the second configuration. But you have to study configurations if you even have that option in your version. The only better solution will be when I have time to learn WizoScript to suppress or unsuppress constraints tagged with "suppress" in the name (Andy?). Restore constraints appears the only resolution.
Different users here use different approaches to defend against software update/loss. Sometimes it actually works. If I were quoted for my most profound professional, (heh,) thought - it would probably be "I was this close...".
I'm afraid I'm a zagger (when everyone else is zigging) so best wishes.
As Lew explains - with these "Standards" organizations the tail is wagging the dog so everyone gets burned. It could even be a case of Geomagic doing something right now that it was doing wrong.