My Illogical Theory
Firstly, they might simply ignore the fact that it was once a pure type and pretend that Ash always knew it was a part Fairy, or better yet didn't know the type at all.
Or, what may happen is that some smart person (like, Brock-smart, not saying Brock will come though) will come along and say that scientists recently discovered that Wigglytuff (for example) is part Fairy-type as well.
I personally believe the first theory is true, but I guess we're gonna have to wait till the debut of the first Fairy-type Pokemon.
Hope I helped. :)