Can Rapid Recovery backup machines over a VPN connection?

Emte is definitely right. You have to treat the VPN as if it is any other network and make sure all the ports are open for the core to contact the agent that's on VPN. Usually by default VPN's don't allow unsolicited communication from the prod network to the VPN network. So definitely start with checking the routing and the ports. For agent based backup you specifically need 8006 for communication and 8009 for data transfer (https://support.quest.com/kb/119905/default-ports-used-by-appassure-and-rapid-recovery).

The other piece is DNS. I assume you have the machines protected via their hostname. When they connect to the VPN is their DNS entry being updated and is the core then able to ping that machine via hostname? If DNS isn't updating dynamically then the core won't ever be able to connect to the machines because it can't ever locate them.

Well, thanks so much. I have enough to chew on for a while! I will pass along the results when I have them. 

Well, thanks so much. I have enough to chew on for a while! I will pass along the results when I have them.