I have the game installed on an external hdd. When I try to run the bat file as normal, it just gives me a permission error: 

Traceback (most recent call last):
  File "K:\Games\Hitman 3\Runtime\Framework\tools\main.py", line 59, in <module>
    shutil.copyfile(os.path.join(temp_dir, 'packagedefinition.txt'),
  File "shutil.py", line 264, in copyfile
PermissionError: [Errno 13] Permission denied: 'K:\\Games\\Hitman 3\\Runtime\\Framework\\tools\\..\\..\\packagedefinition.txt'

When I start the bat in administrator it says the system cannot find the given path. So the way I do it is just open a Admin cmd and then cd into the Framework and then run "tools\thirdparty\python\python.exe tools\main.py" (this is what is in the bat file) and then it works. Very weird

Not sure why that happens. It might work if you give yourself permissions to access all files, then start as regular user?