I was probably being overly cautious (in fact JAL's website spells out the consequences of skiplagging pretty straightforwardly, that it only affects the skiplagged booking), but in my case, I actually was continuing on to another destination on a separate JAL ticket that departed only shortly after the connecting flight. Since those two were at about the same time on the same airline, I wanted to avoid any issues at the airport getting to the flight that I actually wanted to take.