Trying to make a song and the timing is perfect up until it hits a sustain that is longer than the sustain in the song. After that point the rest of the song is off beat and notes dont line up with the music. Is there a tool in EoF I can use to shorten the sustain and line up the notes after the sustain to match the timing of the song?

I guess at that sustain the BPM of the song goes down for the duration of the song. Any way I can change the BPM of the rest of the song after that sustain without messing it up?

I am not really sure what you are talking about cause the way you use the word sustain probably means something different than what you use it for. Maybe screenshot would be a lot more explicit in your case.

I believe he's talking about syncing beats to correct the note positions and durations. You can click and drag a beat marker (-->) to correct its position, and surrounding beats up to the previous and next anchors will have their tempos adjusted accordingly.