Question-A from Site-A is migrated to Site-B . If this question is
Up-voted in Site-B , what site of user's reputation will be increased
When your question is migrated from Site-A it is actually removed from site-A so that means that question is no longer a part of that site because of which it can not have upvotes or downvotes.
Therefore if the question is upvoted in Site-B it will not have effect in your reputation on Site-A
what site of user's reputation will be increased ? Site-A or Site-B ?
As your question is now on site-B the reputation changes for upvotes and downvotes will only be effective for Site-B and not for Site-A where the question was actually asked.
As informed by @ Sha Wiz Dow Ard ,
The question is not removed instantly. It's locked for 30 days and only then deleted (by an automatic process).
The reasoning behind this is to give the target site time to reject the migration (by closing it) then it's rebounded back.