mapping in a clean install is always a good idea.
Not to say that what marko did was right. More like a huge pain in the ass.
If you ever use any texture or shader that doesn’t come with the game, make sure you put it under textures/yourmapname/whatever, or (if it is for something shared among several of your maps) textures/yourmappinghandle/whatever.
Now if you do find yourself with a map that uses a lot of non-standard texuters, search/replace from the texture menu is a very good way to fix it. Assuming both textures are the same size, it keeps all the alignment and such unchanged. Another thing that isn’t immediatly obvious is that you can select the texture to find and the one to replace using the normal texture selection commands (i.e. by selecting a texture in the textures window, or a face in the 3d view)