R1Q2 provides a little-used command called "whereis" that will tell you where a file is loaded from.
Example: You are kicked from a server due to modified models/objects/rocket/tris.md2. Without exiting R1Q2 or changing game, goto the console and type:whereis models/objects/rocket/tris.md2
You will get back the location of the file or pak file from which R1Q2 is currently finding the model:
models/objects/rocket/tris.md2 is found in pakfile ./baseq2/pak0.pak as models/objects/rocket/tris.md2, 2756 bytes.
This should help you out if you have a lot of pak files and don't know where your bad files are coming from.