Parallels 11 - Ctrl / Command key swap

BeauH

Bit poster
Within OSX I have swapped the Ctrl key with the Command key in System Preference > Keyboard > Modifier Keys... > ...
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http://superuser.com/questions/250611/mac-os-change-command-to-control-key
Now within my Windows 10 VM using the normal key combinations don't work i.e. Ctrl Clicking, etc.
If I revert the modifier keys back to normal and don't swap CTRL with COMMAND in OSX system preferences it works as expected.
Is there an easy way to fix the mappings in Parallels given my "System Preference" changes to swap the Ctrl and Command keys?
 
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