[dnanian]

I'm not quite sure what you do and don't have here. Are you backing up to a bundle? Are you backing up bundles on the main drive (you said "Main External HD", so I don't know what that is)? I'm just not clear what you're dealing with here.

If you're trying to back up encrypted bundles, there's no trick: you just make sure they're ejected, and they'll be backed up along with everything else -- no tricks, nothing complicated.