Files= in windows ME problem

I have a computer in the office that accesses a DOS accounting program that is on the network. When the user runs a certain report it says that there are too many files open and the box says files=40. I’ve tried changing the config.sys file in theC:\ directory, every time I reboot the file is overwritten as a blank file and I cannot implement changes. I’m also curious if it even matters if I change the Config.sys file because I’ve heard Windows ME does not access it. I have to get the files= set higher. Any suggestions?