1. Mozy, my backup method, will see this as a deletion and then the files appear in the new location. It does handle this intelligently for larger files, so as to prevent tons of unnecessary data transfer, but it's still a whole lot of work and bandwidth. I decided: so be it. It needs to serve my needs, not the other way around.
2. More critically, Sony Movie Studio Platinum, my video creation software, keeps pointers to old project files when you're using them as part of new projects. They're relative pointers, meaning you can pick up and move an entire directory structure without disruption, if everything's on the same "tree". But what I had to do would disrupt all of this, and I decided to just go ahead, deal with the "pain" once, and tell the software where to find the older components.
As it turns out, the newer version that I recently purchased does a much better job of handling this precise scenario, and once I started telling it where to find certain source files, it correctly figured out that others were the in same relative relationship to the new directories. In the end, I only had to specify the two directory roots that I had moved, and then a whole bunch of confirmation clicks to its (correct) guesses for all of the files beyond that.