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If I'm understanding your question correctly, it sounds like you are trying to open an instance of PSSE and have that instance of PSSE execute a Python script. If an instance of PSSE is already open, then you want to control that instance and get it to execute your Python script. And this is all done by some vba code that creates a Windows batch file.
If that's correct, then your problem is with Windows process management. For security reasons, an operating system won't let one application's process directly interact with another application's process. On other words, you will need to open a new instance of PSSE every time. Windows will not let your vba script look for an open instance of PSSE and directly interact with it.
Elaborate more on what you are trying to accomplish with your vba scipt, and I might be able to help with a workaround.