I understand that ControlThink is working on some software that might perform that type of function. It has not been released yet though.
Unfortunately, the only way I know of, now, to remove a 'completely dead' node is to remove all active nodes, reset your controller, and, start from scratch on building a network. Kind of klunky. If it could still 'talk' you could just do a 'remove node' type operation, I'm guessing you have already tried that.
There may be a super wiz-bang $1000.00 hardware controller out there that already does this type of stuff but my HA budget is limited. I use the battery controllers and some beta ThinkEssentials(tm) software for my control needs at the present time.
If you have any questions about the ControlThink software, they have a forum over at
http://forums.controlthink.com/
Ken
edit corrected spelling