They way it works in pixelmon now is that when you transform it the HP increases based on a multiplier, for example if your Max HP was 300 and becomes 450 after transforming that means that your 300 HP has been multiplite by 1.5x.
Therefore Your remaining HP lets say 100/300 becomes 150/450, or when your HP is really low 20/300 becomes 30/450.
This change would make Zygarde Complete alot more viable and lots more fun to play