You NEED to work out what you did wrong so it doesn't;t come back and bit you all the time. In video editing, going back and forth between programmes and even computers is normal and perfectly quality concious. I edit on one computer either in my video studio or in my audio studio a mile away. I'll grade the edit file, open it on the PC in my audio studio, bring the audio files into cubase on the other PC in the studio, edit, add, tweak and fiddle, then dump it back into the video editor quite transparently. If you had horrible problems, something went wrong. You need to to work out what to make sure when you need to do this, you can. .wav and .mp3 work fine, and cubase can now take in video files and extract the audio if that's useful to you - it just works.