I want to create an iMessage app that allows the user to save stickers, so when a new release of the iMessage app comes out with entirely different stickers the user would be able to use the stickers from the previous version, and so on.
I would also like to know if you can replace an app on iTunes Connect with a different project than the original was built on.
eg. create a game for iOS
a few months later, create the same game for iMessage and iOS but with a new project, and the identifications, profiles and certificates the same as the original.
Not sure if the community can help you with the first part of your question, because it depends on your implementation. Sure it's possible, but you won't be able to use the native UI within iMessage.
Secondary part of your question with regards to updating an app on iTunes Connect: You can always update an app if you use the same bundle ID (com.test.app) and make sure the version and build code are correct. (i.e. increasing) Besides that it does not matter what project / base you are using, if you correctly sign and build the IPA and upload it to iTunes Connect: https://help.apple.com/itunes-connect/developer/#/dev480217e79