http://www.newvegasnexus.com/downloads/file.php?id=42105
Here's a fix! When saying goodbye to Jed Masterson, you have the option of firing all your companions, ED-E Included, and it teleports them back to their home location. Talk to him again, and Voila! you can play Honest Hearts!
I do not know if that fixes ED-E all together, as I don't have the ED-E bug on any save game (which I'm glad about), but if this fixes ED-E for someone, let me know.
other fixes/changes can be seen on the Download page.
