Hi
Is there any visual evidence that the beep is on the soundtrack?
i.e. is a peak is visible? If so split the audio track just before it and mute or delete the section isolated. You can then alter your audio fade suitably. If you think that isn't working then you could delete or mute the offending section a replace it with a copy of a more suitable audio clip or add this to Audio track 2 with a tiny overlap so it blends in.
Nat