Closing 1 excel when multiple instances of excel are open during runtime in QTP

I have written a VB script to batch run the QTP scripts. My VB script takes input from the "ControlFile" excel to get the name of the test script to open and execute in QTP. So I need to keep this "ControlFile" excel open throughout the execution of all the scripts in the batch. The problem is my scripts open some excel for comparison and when they are closed with appexcel.Quit, even my "ControlFile" excel closes and hence I am unable to get the scriptnames after that. The execution stops here. Can anyone please help me with this, to close 1 particular instance of an excel during runtime. Thanks in Advance for the help!

Code
 SystemUtil.CloseProcessByHwnd"Hwndvalue"
Exp:
SystemUtil.CloseProcessByHwnd"132638"