Antoon,
You have discovered a little known disfunction with Flash. After about 2000 frames, Flash will loose sync (consistantly). The solution is to put sync pops at the front and back of the animation. That is a one frame flash frame with an accompaning loud beep of blip. When those are in the Flash file you will be able to sync the audio in AE. Once your new Footage and audio with sync pops are imported in, you will need to use the time streatch funtion in AE to scale the audio. I have found that scene lengths around 6 mins require a squash of 99.8 percent. Apply that to the audio and then synch your front pop. Then check the end pop. You’ll have to finesse it to get it just right. I have asked my pals with real editing systems, Avids and such, and this sorta thing is pretty common place… Getting picture lock is hard, you just have to do the work to get the synch. Let us know if that helps.
-R