I have a map with an alternating texture. If I open the bsp file with Quark, it displays a set of textures, and this particular one is animated, changing regular->red->regular in a 1-second interval.

Now, if I extract it, I get two files:
+0cblack2.jpg
+acblack2.jpg
However, replacing these with two 24 bit textures doesn't work. The game still uses the original ones.

Any ideas?

afaik the format for animated textures is +0texturename.jpg, then +1texturename.jpg and so on. try renaming the 24bit replacement for +acblack2.jpg to +1cblack2.jpg