It's not really a big problem in compairison to other things that could happen, but your triggers won't work any more, so you will want to change them back.
Unless your map has a lot of triggers in it, you could just go back and re-texture all of them, but otherwise, just use the "replace" feature in the texture browser.
All you have to do is select the texture you want to replace (CLIP) in the texture browser, then click "replace" down at the bottom. A screen will pop up, and you can select the texture you want to replace it with (AAATRIGGER). click "Replace" and all the textures in your level that are CLIP will turn into AAATRIGGER textures.
The only problem with this is if you have a lot of CLIP textures in your level, then you'll just have to manually go through and re-texture those...
Hope that helps.