Strange issue we were facing with opening files from SharePoint into its respective MS Office applications after applying new publishing tool and modify the farm to utilize SSL (https).
The issue was “Sorry, we couldn’t open <file url> file”
After, some research we found the resolution:
1- Close all MS Office Applications
2- Open the “Office <Your Version> Upload Center”
3- Click on “Settings”
4- Click on “Delete cached files”
Try again and yes it works 
I hope that helped
Ahmed
