From what I can see by looking around, I don't think there's a solid consensus. Here's a thread on the subject if you'd like to read it.
http://paizo.com/forums/dmtz2ggb?Flying-and-encumbrance
This isn't specifically covered in the RAW. To me, that means it's really up to your DM. Whether he plays a strict or lose game will decide the answer to that, but I have to say that a reduction to a flyer's speed is generally significant enough to make it hard for him to fly already, and the original game designers may well have considered that when they set this all up.