The wish for Youth isn't part of GT. It's only a plot hole if you assume that GT is following the same off-panel events as Super. The first time the Pilaf Gang showed up as children was in Battle of Gods, and that was the first time it was known they wished for youth. Their appearance in GT is irrelevant, since it's a different story entirely.
In the Android Timeline, Goku dies, and stays dead since the dragon balls cant reverse natural death. Time Travel in dragonball works on Multiverse theory. Here's Gohan explaining it, so i don't have to. [
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] Bottom line it, The Androids timeline still exists, even after the Cell Games, and as far as we know, it will continue to exist indefinately.
If we're being techical, the multiple timelines exist seperately from the multiple universes. There should be a 6th Universe in the Androids timeline. But then you realise that there are now 48 universes in Dragonball, and your brain starts hurting.