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In PKHeX go to Settings > Advanced and set AllowIncompatibleConversion to either AllowIncompatibleAll or AllowIncompatibleSane. Some information like the original gen 3 met location get lost on the tranfer up to gen 4 and are not part of the pk4 structure. PKHeX tries to reconstruct those values by getting the first possible match, which might not always be correct. If you do the backwards transfer this Diglett will have a met location of Granite Cave, change that to Diglett's Cave and the mon will be legal.