Ahh I was actually going to recommend something very like that but someone else did all the work.  plink comes with putty and I have used it for automated ssh tasks in order to connect to a linux box, and execute commands based on a windows bat file.  I am not familiar with pscp which that guy uses but I would just have created two cgminer.conf files on the miner, like cgminer.conf.lo and cgminer.conf.hi and use plink to do some sort of copy and rename on the conf files on the miner rather than copy them onto the miner each time.