It had happened to me several times with 5D footage because I was using the program while it did the L&T. The solution is that I don’t use it now and it stop happening, don’t save, cut, rename or anything.
Convert to Prores 422 or LT (they say HQ is too much) via log and transfer if you leaved the card structure intact if not use mpge streamclip or compressor.
Then edit with that and convert it at the end to your delivery codec, you can do it with compressor or vÃa final.
Good luck.
I wouldn’t think you can’t hear audio from a video card.
Maybe I am missunderstaning but you are saying that no audio comes from the mini display port of your video card?