I could be wrong but I am assuming you are just changing the data on another Frogadier to match the Friend Safari and that is why it is causing problem. If that is true, then what you could do is open Tools>Data>Encounter Database and then search for Frogadier.
Make sure you unblock the plugin via Right Click->Properties over the plugins.
Also, how are you loading your save? Make sure you open a window of PKHeX first, then drag the save in; as opposed to double clicking your save to open PKHeX.