Hypothetical situation:
>character attacks an enemy
>GM upgrades the difficulty of the check via Dark Side token
>character uses the Natural Marksman ability (reroll any Ranged [light] or Ranged [heavy] check once per session)
Is the difficulty still upgraded?

And also, if the GM didn't upgrade the difficulty on the first go 'round, could he upgrade it on the reroll?

I think the book says that the re-roll is done with exactly the same dice pool, so I'd say the dark side upgrade counts. Similarly, as a GM I wouldn't upgrade the second roll.

Do you think it works the same for players and Light Side tokens?

You mean when a GM character makes a re-roll and players upgrade the difficulty? If yes, then yeah, the same principle applies - a re-roll is made with exactly the same pool of dice as the original roll.

I meant when a player uses a Light Side token to upgrade his Ranged check. He keeps that upgrade for the reroll, but can't add one in if the first roll didn't use one?

That's how I'd rule it. Of course if I'm being a benevolent GM and the situation was really important (not just A shot among many) I could agree to an upgrade in the re-roll, but saying that it's an exception.

That's how we do it. Any and all previously expended upgrades, downgrades, and destiny points apply as before. The roller picks up the exact same pile and throws again.