The Dutch appeal court has ruled that flying over the Natura 2000 aera of the Oostvaarders plassen does not constitute a disturbance of wildlife.
Actually the findings of the court were slightly different.
The courts interpretation of the Flora- and Fauna law is that it's aimed at long-lasting protection of wildlife areas. To be prosecuted under the law requires a long lasting or serious disturbance of the wildlife sanctuary, where the ecosystem may suffer long-term effects.
The most important sentence is probably this:
Sporadische verstoringen zonder enige waarschijnlijke negatieve invloed worden niet beschouwd als een verstoring in de zin van de Flora- en faunawet.
("Sporadic disturbance without any probable negative influences will not be considered a disturbance under the Flora- and Fauna law.")
So the court did acknowledge the rangers finding that the pilots actually caused a disturbance (birds taking flight), but didn't find the disturbance severe enough to cause long-lasting effect to the ecosystem. And thus finds the disturbance not punishable under the Flora- and Fauna law.
In the long run, the court has now placed a significant limit on the application of the Flora- and Faunalaw. Whereas previously any disturbance was cause for prosecution, the prosecutor now has to prove a long-lasting effect on the ecosystem.
All in all a very happy ending. Both for the pilots involved (a conviction, even without punishment, would give them a criminal record) and for aviation in general.