Hi Steve, as I understand it you will effectively be running two separate Wi-Fi networks and therefore when clients need to roam they will disconnect from one LAN and need to re-associate with the other LAN.
Wi-Fi roam-assist mechanisms such as 802.11k, r and v are usually implemented in the controller software and as the virtual controllers won't be aware of the other APs, these mechanisms won't operate.
Have you considered implementing a Wireless LAN Controller (e.g. RFS4000) that can adopt both the older and new APs to remedy this situation?
Hope that helps.
Best regards,
Darrel.