Can I release Swift implementation of an application over the Xamarin implementation in Apple store?
Sure - the store delivers binary content that it code signs as complete so it doesn’t matter how you got the submission to Apple. 

Now, the end user experience could still be a mess if you don’t have a smooth migration plan for app data, settings and what happens when someone restores a backup from 6 months ago onto the new version of the app. Those things are hard to test, possibly difficult to program and not something that was designed into your data model currently.