I've been able to work around this by the following:
Change the split tunnel to force traffic to the external IP of the agent handler through the VPN tunnel.
Create a Windows Firewall rule on the agent handler blocking TCP 80 and 443 from VPN and internal network subnets.
This essentially allows clients to connect to the agent handler when not on VPN or internal network, but blocks access to the agent handler once they connect to VPN or an internal network (be sure not to include the subnet your ePO server is on as it still needs to be able to communicate with the agent handler).
I've noticed that the agent will continue to try to connect to the agent handler and not immediately switch to the ePO server. It seems to take two ASCI before it will switch over. So, up to two hours with the default ASCI. We're a small company (under 600 clients) so I may lower the ASCI to 30 min to force the change quicker.
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