First, please tell us the format/CODEC of your original footage. Is it HD, or SD?
I use DigitalMedia Converter (!US$50), but there are plenty of freeware converters out there. To date, DMC has been perfect about 99% of the time.
I use SD material, and can batch convert to DV-AVI Type II w/ 48KHz 16-bit PCM/WAV Audio, for Import to PrPro.
Your exact file formats/CODEC might dictate something else.