I'm making progress here. Do I need two separate copies of BFGMiner on the hard drive to run 2 instances? What happens to config file if I run 2 instances from one copy?
You definitely need 2 separate copies in different folders.
In my case, I only use one copy since I don't run the instances off of a config file. I just input the parameters as a shortcut target of bfgminer.exe (i.e. one shortcut with BE options and another with BFL options...and so on and so forth).
If you run from *.bat files, then place the shortcuts on the desktop, then it should work ok.
To be on the safe side, for the bfl device, specify the com port number in the second *.bat file. That way you know its not even looking at anything else.
I don't use .bat files either. I just use a shortcut with specific parameters for each instance; and yes, they're conveniently placed on the desktop. In my case, I run the BE array first with its specific shortcut while the BFL device is turned off. When the BE array is running and has settled, I then turn on the BFL device and run its specific shortcut. Though the BFL device would run with the BE array in one instance using the BE-specific shortcut (-S all), BFGMiner would identify its chips as BE devices and would label it as such (ICA##).