Both the blade and the face of the guard should be completely finished when the guard goes on for the last time.
In my shop, damascus guards get finished to 400-600 grit, other metals get finished to 800 or 1000 grit.
May I ask how it is that the faces are getting scratched up during finishing? With the blade and guard face completely finished, if you're still getting scratches, I'd re-evaluate the rest of my finishing process.
If you do get a small scratch or scuff on the face after it's all finished, as hard as it is, I've come to just leave it alone. In my experiences, trying to fix it at that point will only make it worse. It would, of course, depend on what type of scratch and how bad we're talking about.
I've tried the taping up the ricasso carefully and sanding with steel wool, q-tips, popsicle sticks with sandpaper around them etc....and I've never gotten results that were satisfactory to me, hence the decision to leave it alone.