Is it best to leave the ID the same so it overwrites one. For example: Somebody tried my free version and decided to get the paid one and it overwrites the free version but keeps the save file.
As i know, if you want to publish your game to google play or appstore, this will be impossible to do how you want, the user that decided to upgrade to paid version will just download the paid version as a second app, no replacing will be done, all apps uploaded to google play and appstore are always different, there's no way to publish two apps with a same signed ID, it's always different. But, you can upload both apps, free and paid, just make in-app purchase in your free app that will disable the ads.