I have cross bred a female Skarmory, with a male Altaria, so the baby Skarmory, was born with the moves:

Leer, Peck and SKY ATTACK.

Sky Attack was the move Altaria knew.

I put the baby Skarmory in Day-Care, knowing that sooner or later the move will be overwritten by a new move.

So I went out and stole a heart scale from a Wild Luvdisc.
So I could re-teach the move when I go to the move-tutor.

Later, I took out my baby Sakrmaory and sure enough it had forgotton Sky Attack.
So I went to the Move-Tutor to ask for a re-teach, and he couldn't teach baby Skarmory Sky Attack, presumably because it was unnatural to him because he was a cross breed.

I still have the adult Skarmory and Altaria, so I can continue making eggs, but I don't want to teach him up to level 45. (Which is when he learns his last move, Metal Sound.) So is there any way I can protect a move from being overwritten, or at least ALL of the moves to be protected from over writing.

Thanks.

I think the breeder deletes moves either by oldest move or bottom move. If they delete the bottom move, then every once in a while you can drop in and reorder his or her moves.

i.e., When Sky Attack gets to the bottom of the movelist, reorder it to the top of the movelist.

EDIT: V Cool, I had it backwards then. And I don't think I made myself clear at all. Thanks. V

If your moves are like :
Peck
Leer
Agility
Sky attack

...then Peck will be forgotten first.
And the move-tutor that can teach old moves can only teach those moves the Pokemon learned by leveling up, and not in any other way.