Hi John,
I was able to reproduce this behavior with MiningBuilding Blueprint in 4.7.3, and I’ve entered a bug report for issue (UE-12129). I included a copy of project so developers have something to work with. I’ll let you know as soon as I see any update on it. For now, it doesn’t appear to be causing any issues during PIE, so you should be able to work around it (aside from mild annoyance of having to click Yes button before PIE every time).
I also checked this in 4.8, and compiling same Blueprint crashed editor. I’ve included that information in bug report, but I wanted to make sure you’re aware of it. Hopefully fixing one issue will also fix other.
I’m not sure what’s causing a long compile time for you, though. It’s definitely doing something, but I’m only getting a few seconds delay at most. You might try removing Intermediate and Saved folders from your project (make a copy somewhere, first!).