AFAIK the default for Quit the Viewer has always been Ctrl+Q.
So, I suspect your Ctrl+W would have been your customisation.
If you upgraded from 4.? to 6.? on the same machine your customisations should have been retained. Ditto if you used calibre's export/import tools to move you libraries and configuration to another computer.
As has been pointed out, Ctrl+W is most often used for closing the current tab panel in editors, browsers and such like. I use Escape to Quit the Viewer, or Alt+Space, C.
BR