What's up with the YouTube Audio Editor?

So we shot a documentary. A lot of work went into it. I chose to use an audio track that I felt may not be copyrighted being that I found it on a site that "claimed" it was remixed so it was royalty free. Apparently YouTube did not feel the same. Anyway, Long story short after uploading and seeing it gain traction it received a copyright claim. I'm not in trouble or anything, But am now unable to receive any monetary value for the video.

Upon trying to edit the audio track out and replace it with another song, It completely removed the audio from the rest of the video. Does anyone have any tips on how to prevent this or include the original track without the song? Any help would be greatly appreciated!