I don't think a batch file can interact with a GUI. Normally a batch file will set or unset some property which gets reflected in the GUI as checked or unchecked. If you batch file only interacts with one connection, the others will be left alone.
It does seem to look that way. I was hoping that you could just disconnect them then at the end call another batch file that reconnects them. Looks like i will have to look into it and doing it with some scripting language. Thanks For the reply.