Yes, to switch the card being emulated, you can flash new firmware images directly from DOS using the pgusinit.exe program that ships in the release package. It takes about 5 seconds to load the firmware and the new emulation is available to use right away without needing to reboot the machine.

Longer-term, I'd like to have multiple cores available in one firmware image for the ability to instantly enable/disable them. All code runs from RAM instead of flash for speed, so that's a potential limitation on the number of cores that can be loaded simultaneously.