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When writing to a file or pipe, cmd's internal commands default to either the current codepage of the attached console or, for a detached process, the system locale codepage. It uses a best-fit encoding that tries to map characters to similar characters in the codepage. For example:
 >>> win_unicode_console.enable()
 >>> os.environ['TEST©'] = '®'
 >>> out = subprocess.check_output('cmd /c set test')
 >>> out.decode(sys.__stdout__.encoding).strip()
 'TESTc=r'
You can force it to use Unicode (UTF-16LE) with the /u option:
 >>> out = subprocess.check_output('cmd /u /c set test')
 >>> out.decode('utf-16le').strip()
 'TEST©=®'
subprocess could use "/u /c" instead of "/c". This would only affect the output of internal shell commands such as "dir" and "set".