Most likely the sqrl miner will include the bitstreams needed, when you boot your rig the fpga will be empty, a bitstream fitting the algo youre mining will be loaded each time the miner starts, so it will include multiple bitstreams.

And yes if the change is just meant to kick of asics again or discourage development, it will be small, but the question is how does the cryptonight comunity feel about this, do they wana fork to get rid of fpga's next time also by choosing a complete other algo?