What i do to counter this problem is i delete the line for the pokemon that is in, then disable all the codes, i then enter a battle to make sure it changed back to default, then after the batter i enable all the codes then put in the new pokemon code for a new pokemon to catch.
be sure you delete the old pokemon line because, in my experence atleast, when I had the other one still there but disabled, it still ran somehow.


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