Assuming the light under the ledge isn't enough for the coral to use, the tissue on those branches will begin to die back and eventually the branch will be dead. Easiest thing is to just frag (cut) those branches and either relocate them or turn them in for credit at your LFS.
As corals grow, they'll end up shading themselves too. Lower branches will die off as the new growth shades them, unless you prune the new growth to allow light to penetrate.