Well, there will be a new noggit version in the (near) future, wait for it. With it the texture swaping will be much easier : D ( as the Video shows.
Just try to work on the other parts first and if you have to work on the "damaged" ones, change the texture for every chunk..
But post also your logfile and your config just as Steff had said to solve the problem and if there will be someone with the same problem, he/she can solve this faster^^