I would transfer the data to an another computer or a harddrive, and format your computer. Sometimes, there´s just no other way, and backup is always a good idea anyway.
it may be quicker to just do it than keep avoiding it...back up the essentials, and 'flatten and rebuild'
jfyi amongst my colleagues (biiig software company you've heard of) it is common knowledge that F&R is the best answer to this king of problem every time.