Try to open map in SDL 1.2, delete textures from corrupted chunks and apply new ones via SDL 1.2. Deleting textures in SDL 1.3 may corrupt all deleted textures on the whole ADT, but I wasn't able to replicate bug and find out when and why it happens.
I used offset fixed copies of QA_DVD ADTs and if my memory still serves well, it happened when I painted textures, did something on the ADT and without first saving/restarting noggit after first applying textures on ADT I tryed to delete some of the textures via standart ctr+shift+click. Then all textures I wanted to delete turned white. I think they were set to "" or something like that, not to (null). Just guessing. Like I said, SDL 1.2 can deal wth it, SDL 1.3 can't.