appeal play

[bbman]

Situation:
No outs, R3 on third (no other runners on base). Fly ball to F8, R3 apparently tags up and scores. Defense wants to appeal the tag up. F1 engages the pitching plate (with ball and no time out had been called), and without disengaging, steps and throws over to third, but throw goes over F5's head and rolls against fence.
What's the proper call?
Does pitcher have to disengage to make a proper appeal play (because he can't legally throw to an unoccupied base)?
Would the call be different in mlb vs high school?
Thanks in advance