did you find a solution to this? i’m having the same situation.
my 2nd store’s homepage redirects to the 1st stores homepage.
and all other https files within magento on the 2nd store give a 404 error.
however, a regular file loaded onto the 2nd store’s folder comes up just fine in https
so it’s not a certificate issue. it’s some sort of redirect / rewrite issue in magento....