This is the exact reason very clients maintain their support contracts. This needs to be reported if for no other reason to have PTC acknowledge that these types of things are still happening; just in case someone snuck in there and ticked off the "done" box on something that is far from resolved.
Patrick, what version are you using?
I still have a nasty bug on patterned features that would disappear instances on random locations of the pattern. I drove that one through support team to resolve. They said it was resolved in M050 and sure enough, it popped back up in M090 IIRC. Sometimes it is easier to live with a bug than to find new ones that stop you dead in your tracks.
The only other option is a revolve. Again, none of this should be necessary. As Doug said, you may have to backtrack to the place the hole surface was created. Most likely, this is the culprit. You can also try moving the pilot holes to after these hole features or removing them all together. I have seen instances in some functions that did not like origins floating in space. Something like the Auto Remove switch setting can get confused.
Anyway, I hope you get a chance to report it and let PTC fix their issues. When I have a feature I need, I don't like having to tweak it just so the software will accept it.