I know this is way late, but I found this because I had the same question. In case anybody else is worried about it and comes searching, I can confirm that clicking skip only cycles through the missions that are displayed.
If you're like me and don't live in any of the areas that have map missions, you can click skip to remove the map mission and replace it with a different mission. You will not lose the mission you skipped, however. Skip or complete more missions to cycle it back to the visible list.
I hope this ends up being helpful to someone eventually!