I was just wondering how Windows behaved during updates, etc. All I could find on Microsoft forms was the _advice_ not to do it. _advice_ is nice but it's not really an explanation.
I didn't want to respond until I'd had a reasonable amount of time to test things out, since I'd only recently moved my folders. Everything has been working fine, with one exception: some updates (specifically, those related to internet explorer) failed with error 80070011. It turns out Windows 7 has some entries in the registry that need to be altered if you move your program files with a junction. I found this solution which solved those issues for me.