Get them back together in your place and do a proper recording. Run the video camera at the same time for a later sync/DVD release.Like the Gambler says, you got to know when to hold 'um, know when to fold 'um...
Then it's time your ask your friend whether they want to scrap the entire thing or do a proper job. If you explain the original recording is toast, they may accept those facts.
I get material like this in all the time so I am going to keep playing with this particular project until I find some solution for the next time.
It's impossible to say something valuable without hearing the program. It really depends if the affected section is the only flute or other instruments are also playing when distortion is taking place, and so on.For solo instruments I used spectral repair successfully and sometimes simple lpf, too. I also replaced damaged repetitive parts with good ones- the most time consuming was looking for a proper replacement source, including start and end points within the same audio track. This method is usually useless with live recording (because the same parts usually varies each time when performed live) but sometimes works for studio work.Art