Command+s does the same thing as command+shift+s when saving files that were created in an older version of indd. It creates a dialogue box and a "are you sure you want to overwrite"
This is a useless (expected, i have been told by support) behavior that only slows things down when revising large amounts of files.
Its because it updates the file to run smoothly, but who would then not want to save it into the updated version? command+s should just overwrite/create the new version file automatically. If need be there could be a warning dialogue the first time with a checkbox to avoid it in the future