I'm using FS2004 (FS9) & I've downloaded 2 helo's & a prop (Pitts Special), that were designed for FS2002. The models look good & work correctly except for their propeller & rotor blades... basically they aren't there, although their textures etc are all in the download.

I've created a new texture for the Pitts Special & still nothing appears on the models prop.

Is there any way of editing the .cfg or .air files to solve this?

Your model was probably built with FSDS1 or AF99, which, while FS2002 supported those models, FS2004 does not.

Some animated parts, as you've seen, don't show up.

Without the source file modified and recompilied for FS2004, there's not much you can do.