One of my band parents had the idea of draping our timpani with a material made to match our uniforms and to hide the beat up shells.  I am afraid this will affect resonance and projection on the field

Thoughts?

I don't think it should be a problem as the sound is being projected from the head. As long as the drapes don't touch the heads or the shells you should be fine.

If you have drums with outboard hardware and spiders outside the bowls, then draping material from the outboard supports is the way to go.

If you have center-supported timpani with the spiders inside the bowls, then it will be hard to drape anything without contacting the bowls. I'm not convinced that this would be a bad thing, but it may be. I have a feeling timpani bowls are heavy enough and rigid enough that damping them won't be noticeable. That should be easy enough to check with an old blanket.