Eryk Sun added the comment:

Let's do a bit of house cleaning. Run the following commands in a command 
prompt:

    reg delete HKCU\SOFTWARE\Classes\.py /f
    reg delete HKCU\SOFTWARE\Classes\py_auto_file /f
    reg delete HKCU\SOFTWARE\Classes\Applications\python.exe /f
    reg delete HKCU\SOFTWARE\Classes\Applications\py.exe /f
    reg delete 
HKCU\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\FileExts\.py /f

HKCU\SOFTWARE\Classes\.py is selecting the PyCharm2016.3 ProgId. This takes 
precedence over HKLM\SOFTWARE\Classes\.py, the key that selects Python.File. I 
expect this causes Explorer to automatically reselect the PyCharm2016.3 ProgId. 
Deleting it in combination with deleting "...\Explorer\FileExts\.py" may fix 
the problem, i.e. restore the Edit with IDLE menu.

The "...\Applications\python.exe" and "...\Applications\py.exe" keys were 
created by manually associating with the given executable. Note how the open 
commands have the script path (%1) but no command-line arguments (%*). It's 
harmless to delete these keys.

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nosy: +eryksun

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<http://bugs.python.org/issue29014>
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