What engine do you have?
I have a 2001 Challenger and it has a Mercury SportJet engine. The "four beeps" signal is not associated with the neutral switch. If you're not in neutral, the engine won't crank but you don't get any other indication. Trust me, I've been though that system thoroughly while troubleshooting a bad neutral switch connection. Even with the wire completely disconnected you don't get four beeps... the only symptom is that your engine won't crank.
In 2001 Seadoo made the Challenger 1800 and the Challenger 2000, both with SportJets. I can't remember if there was a Rotax "Challenger" or not. If there was, its beeping patterns may be entirely different.