I saw him two different times in the game. Once while I was leveling up to enter the pre-gym (which was right after defeating Miror B.) and the second was leveling up for Realgam tower to fight the mayor.

Thats why I had no idea about the two females coming back....luckily they did though...I was almost toast for getting Ho-Oh.

I have 11/48 pure....this may take awhile.