From your post:
"I get that warning that some of my documents may not run"
In many instances programs are built upon programs. Programmers do not always start from the very beginning when creating a program they just add to a version they've already created. That's why sometimes you can't remove the older programs because the newer version is relying on it. Generally if you right click on a programs and choose properties there is a tab marked "Dependencies". If something is listed here don't remove it. If nothing is listed here sometimes you can remove it, others times you can't. It's best to just leave them alone. Sorry, it isn't any simpler then that. That's just the way it is (Shrug).
This thread is not being tracked. That's all the information I have.
When you download updates to programs (like a 5.1 version) and the old program is still there (a 4.1) is it safe to get rid of the older version? It seems silly, but when I think about getting rid of some of these I get that warning that some of my documents may not run. I went to Catholic school and so I'm obedient and I leave it there, but my files are really cluttered up and I'd like to clean them up.