Just signed up to help you here.
The main issue is that the flip cameras are notorious for sync drift. I used one to record a 50 minute band recording, and it was painful syncing it after. Certainly doable, but pluraleyes isn’t going to help, so you’ll have to manually nudge it into place.
Ok – so your project is set up to 48kHz? Well your first issue is that the flip’s audio is 44.1kHz, so that might need converting. A quick way to get the flip video in sync with your separate audio is to speed it up slightly. I think my flip camera needs its speed adjusting to something daft like 100.02%.
Obviously it was easier for me as I had a long recording so the drift was much easier.
Hope that helps!