I recall you have a Roadster (be easier if you listed that fact under your avatar.....
). The ATRE if it's set on 3 will be telling the bike it's in 4th gear all the time. When you replaced the battery did you also reset the GIPro? Several of the settings - can't recall which does what now - mine's on 3 all the time) make the ECU believe the bike's in 4th regardles of which gear you're in. Maybe you had it set differently before......???? As you say you're getting N, I'd say that's what has happened.
Edit: and I'd say you can't do much about it other than set the ATRE on a different setting or get rid of it and de-restrict the bike using TuneECU.