Situation
I have a 3rd party GUI application that accepts multiple files via CLI, for example:
MyProgram.exe \"file1\" \
Why not write a .exe with Make single instance application checked.
Then in that new application catch the MyApplication_StartupNextInstance as provided in the MyApplication class to catch all files being pushed by explorer, maybe let the application wait a second or 2 to make sure no following files are being sent by explorer and then combine those all into 1 string and parse them to your 3rd party app.
If interested i can place some code getting you started