yeah, I would just leave it as a skip and mention it in the notes. I did a similar thing once with my D8. I thought I pushed the button to turn on the backlight, and when the light didn't come on, I realized that I had paused the deck. a little note in the text file and that was that. oh well.
or what you could do is cross-fade the two parts and see how it sounds. if it sounds less disruptive that way, go with it. otherwise, just stick with what you've got...