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John temporarily disappears if you are around the storyline area where the sages send you home and you obtain Mewtwo (because John appears back in town after that incident). Once you complete that part John will reappear in the Blackfell Pokemon Center.
I'm not a developer.
Only one sage will appear at a time and they will disappear if you have found them in the past. Just look for the sages in order and you should be able to find them. Here is a guide about the sages: viewtopic.php?f=19&t=11227.
Don't be afraid to be a Skitty in a world of Meowths.
Sending well wishes to everyone.