Were you able to find a solution to this?
I'm having the same problem: I rewrote my Angular to React Native and I'm using the same bundle ID. However, when I archive and distribute the project it's throwing an error saying the bundle ID is already being used by another app in AppStoreConnect, which is in fact the app I'm trying to update.
Are there any specific changes I need to make in the app config for AppStoreConnect to treat this as an update instead of a new submission? As I said the app bundle matches the one that's already online.