I often use PKHeX, and downloaded the latest version today. The Legality Checker is a great tool, it helps a lot.
Flabébé & Pumpkaboo
In XY, I caught a Level 14 Orange Flabébé on Route 7. According to Encounter Tables, Orange Flabébé can only be found at Level 13, but other forms can be found at Level 14. But using a leading Pokémon with the ability Pressure (Hustle and Vital Spirit also work), when encoutering a specific species, there is a 50% chance of having the maximum level of the said species (different forms are treated as same species). This is how it is possible to meet an Orange Flabébé at Level 14.
I did that and then checked with the Legality Checker, which considers it as not valid (Not a valid encounter).
[ATTACH=CONFIG]13157[/ATTACH][ATTACH=CONFIG]13158[/ATTACH]
For Pumpkaboo on Route 16, all forms are considered valid at levels 34-36.
White/Black Flute
In ORAS, the White/Black Flute decreases/increases the level of wild Pokémon (up to 4 according to what I can observe in-game).
White Flute
I first caught a Level 1 Zigzagoon in a Horde on Route 101, found using the White Flute. The Legality Checker considers it as invalid Pokémon (Not a valid encounter).
[ATTACH=CONFIG]13160[/ATTACH][ATTACH=CONFIG]13161[/ATTACH]
I then caught a Level 5 Swablu in a Horde on Route 114, also found using the White Flute. Considered not valid by the Legality Checker.
[ATTACH=CONFIG]13159[/ATTACH][ATTACH=CONFIG]13162[/ATTACH]
Finally, I caught a Level 13 Lombre on Route 114, again using the White Flute. Considered not valid but with two reasons this time ("Not a valid encounter" and "Level is below evolution requirements")
[ATTACH=CONFIG]13163[/ATTACH][ATTACH=CONFIG]13164[/ATTACH]
Black Flute
I caught only one Pokémon here, a Level 13 Swablu, in a Horde on Route 114. This time, it is detected as valid. But the Legality Checker recognized it as a DexNav Encounter (Is it possible to get this level with DexNav ?)
[ATTACH=CONFIG]13155[/ATTACH][ATTACH=CONFIG]13156[/ATTACH]
If I use the Black Flute, almost every Pokémon I capture are considered legal. It is considered as being a DexNav Pokémon, even without the first relearn move.
Friend Safari Floette
It says that Blue and Yellow are invalid and Orange and White are valid. Not supposed to be the opposite ?
