Reply to Problems with S4 Track Prep Tools Mapping

I tried to find a thread with any questions before starting this but I didn't find one, but if there is I will happily direct my question there.

So I downloaded the mapping and prepped around 50 tracks and it worked amazingly! Thanks Ean!

Only problem was when it was time for my gig that evening and I went back to the stock S4 factory mapping all the settings for the Track Prep mapping were still there. The right side worked just fine and I could DJ from it, but the left side still thought I was mapping tracks. I even downloaded the DJTT S4 mapping and imported it to try and over-ride the Track Prep one but that didn't work either. The only way I could get rid of it was to delete every mapping I had and re-install the stock S4 one through the Service Center. I'd like to use this tool to map the rest of my 500 tracks but I'm obviously apprehensive about installing it again.

So my question is has anyone had this problem before, if you have what steps can I take to guard against this or am I just doing something wrong altogether?

Thanks for the help!