Two comments about the Prayer of Manasseh. First, a Hebrew version of it does survive. It was recovered from the Cairo Geniza. But it is clearly a translation into Hebrew from the (original?) Greek version (and perhaps the Syriac), so Phil's point remains sound.
Second, I have argued the possibility that the Prayer of Manasseh is a Christian rather than Jewish composition. I mentioned that article here.
Visit PaleoJudaica daily for the latest news on ancient Judaism and the biblical world.