If you are changing scripts, to avoid having to restart doom3 and reload a saved game, it's usually fastest to run in windowed mode (alt+enter) drop to console, then type

reloadScripts
map testmaps/test_box
give all

(you may need to drop to console for each line).

How do you save the .pk4 while the game is open?

by the way, i found the command is reloadScript

You don't save the .pk4, you operate from raw files in the correct folder structure (i.e. Doom3\base\defs, etc.).

just unpack the files you need and put them where they are supposed to go (folder wise) and you should be set. You should only mess with making a pk4 whith a release version.

yeah, i tried that, but the files were being ignored - weird, i'll give it another go when i have to alter the mod for any reason

odd... you SURE you have the folder structure correct? i.e. NOT Doom3\base\pak000\def but Doom3\base\def

Yep, that's what i had...

so you had the right one or the wrong one?

if you had the right one, I really have no idea what's going on. it should be parsing the raw files and using them preferentially over the pk4'd ones. You sure all your files are named correctly?