Altremote_Update Multiple FPGA's

I have a board currently being used on a previous project with a cyclone III and cyclone II being configured from the same EPCS device (AS). I would like to utilize this board on new design with the Altremote_Update Megafunction in the cyclone III. I am using custom code to control the Megafunction that has been proven in other designs. When the reconfig occurs it always reverts back to the factory default program.

Has anyone tried this before? Is it possible given the cyclone II does not support this Megafunction?