The CM patch uninstall works fine for the program. The trouble is with your characters. The CM patch has quests and items that do not appear in the plain I&B. If you start a character with CM stuff in the plain I&B, unexpected results may occur. I cannot be more specific, since I have never done it.
Most of the CM patch quests do not appear automatically in your logbook. They are either additional steps to existing quests, or stand alone quests with their own quest givers.
Yes, the employees for the Epic Office quest do show up on the map with the CM patch installed.
Personally, with Closed Net gone, I cannot think of a reason most players would not run the CM patch.