I created two waypoints that were based on a plane called “Mount”, which is 400mm above the Base. After I edited Mount to 300mm above the base, I went to run the program and the waypoints did not shift down like I expected it to. It just stays the same as if I never edited it. Did I do something wrong or is this a bug?
It sounds like you did the right thing. 
If you attach your program and installation files, I or someone else might be able to take a look and see if we can see anything wrong with it.