Do as Zane suggests - use Compressor. I did this a couple of weeks ago. I turned the Flip files into ProRes and the quality was surprisingly good. Be sure to turn Frame Controls On (in Compressor's Inspector) and set all quality options to Best.
MacPro 8-core 2.8GHz 8 GB RAM OS 10.5.5 QT7.5.5 Kona 3 Dual Cinema 23 ATI Radeon HD 3870, 24" TV-Logic Monitor, ATTO ExpressSAS R380 RAID Adapter, PDE enclosure with 8-drive 6TB RAID 5
FCS 2 (FCP 6.0.5, Comp 3.0.5, DVDSP 4.2.1, Color 1.0.3)
Pro Tools HD w SYNC IO, Yamaha DM1000, Millennia Media HV-3C, Neumann U87, Schoeps Mk41 mics, Genelec Monitors, PrimaLT ISDN