Hey Alex,
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You suggested 'changing MSEL'. Altera states the MSEL pins should be connected directly to VCCA or GND and therefore should not be connected to any circuitry that can change them.
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I recently submitted a SR asking when the MSEL pins are sampled, and whether I could change the MSEL pin state, whilst holding the FPGA in reset, eg., so I could AS or PS mode configure a Cyclone IV. I was directed to this interesting KB entry:
http://www.altera.com/support/kdb/solutions/rd04032002_3872.html So you can change the MSEL pins, but only before the FPGA actually configures. Changing the MSEL pins after it has read them will have no effect.
I'm posting this here, since you might find it useful :)
Cheers,
Dave