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.
Oh that was your script. I didn't notice that the link in this thread and the other post were both the same person.
Yeah I figured it was a local copy, I was just commenting about how I would have tackled it. The older antminers had a cron tab where you could put commands and schedule them. I used to schedule cgminer restarts in there. That could have been used to accomplish this too but alas, not on a new antminer. I suppose doing the copy from the PC might wind up being better also if the local versions of the cgminer.conf were wiped out by a reboot. I know most of the file system changes get lost when you reboot the miners, can't remember which ones exactly. I thought I saw someone post that there was at least one dir where changes persisted on reboots but not sure which.