We are designing a development board for internal use that will allow us to test the BGA and Module version of the PSoC BLE one at a time and from one MiniProg, one set of sensors on the i2c bus etc. Would having a switch to power down one PSoC allow the other (which is powered on) to be programed ok? We could then flip the switch and perform the same test on the other PSoC.
Depending on how you wire up the switch to switch between the two chips and "disconnect" it from power/the miniprog wire connections, I suspect it would work out fine.
The main concern would be having some pins connected that float the voltage of the chip without fully disconnecting it from power.