You're pretty much screwed with re/installing anything after a
BWP install anyway, moreover if it's biffed at the end. Not running cleanup tool just makes it easier for debugging with backed-up files.
I ran it to free space to allow some more cache for a smoother game as I encountered no bugs but just some lag in large fights with lots of magic; my computer runs with about 20Gb of free HD space lately...
Also found out with that install that a tactics install with BP AI is more stable in these heavy-magic fights that a standard+
SCS AI one... on my computer at least. In previous installs game would hang almost everytime more than 2-3 spells were cast during the same round, that was really aggravating for gameplay