You have to watch out. AA will remove the stains -- redissolve the metal into your pool water -- but the metal is ALL still in your pool. Adding chlorine and raising the pH tends to make it come back OUT of your water. Some will end up on the filter, but it's also likely that your stains may begin to re-appear.

You can minimize this by
+ running your filter 24/7
+ raising the pH and chlorine gradually.
+ using a no-copper algaecide to prevent algae while the chlorine is low.