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I pressume you run (g)Vim with a shortcut.

1. there is current working directory in vim :lcd to see it and :lcd dir to change it. (if you run (g)vim.exe or shortcut it would be path to (g)vim executable)
2. depending on how your python script is implemented, it might read this json file from current working directory (it is inherited by :!) not from your script location directory.

so either change current working direcory :lcd path/to/your/python/script/ or change your python script to read file relative to script location.