EPCS controller and multiple CPUs

You can do this, but you must be very careful about sharing the component between the 2 CPUs. If they both try to access the EPCS at the same time you'll get ugly results. You'd have to add a hardware mutex to control access to the chip, and probably modify the bootloader to use it.

The default EPCS bootloader only supports one software image, placed right after the FPGA image. You'd have to modify it also to load another software image.

Another solution would be to have only one CPU connected to the flash, and have it load the software for the second CPU.