It seems obvious at this point, that there will be little things that the characters notice in their flash-sidewayseseses, that don't add up, evidence of events in their life (that happened on the island) that they don't remember.
It will add up to them realizing, something happened, and that they're not where they belong, and it culminates in the two realities merging, whether it be flash Jack dying, island Hurley dying, what have you until the universe evens itself out.
On a side note, I think the proof that Jacob is the good guy is his speech to Hurley, "Sometimes you can hop in the back of somebody's cab and tell them what to do, other times you just have to let them stare at the ocean until they figure it out". Maybe it's just me and my worldview, I believe you have free will, but at the same time, your life does have a pre-determined endpoint, but you can get there any way you like.
I guess that means if Jacob turns out to be a bad guy, my world will be shattered.