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I have a Jaya, Venerated Firemage in play and cast Chandra's Pyrohelix, targetting two creatures.

Jaya's static ability reads:
If another red source you control would deal damage to a permanent or player, it deals that much damage plus 1 to that permanent or player instead.

Pyrohelix reads:
Chandra's Pyrohelix deals 2 damage divided as you choose among one or two targets.

Does this mean that the two targets both get dealt two damage, because 1 damage gets replaced by 1+1 damage, so Pyrohelix deals four damage in total?

It would be four damage; this is indicated in the rulings below the card on Gatherer:

If damage dealt by a source you control is being divided or assigned among multiple permanents an opponent controls or among an opponent and one or more permanents they control simultaneously, divide the original amount before adding 1. For example, if you attack with a 5/5 red creature with trample and your opponent blocks with a 2/2 creature, you can assign 2 damage to the blocker and 3 damage to the defending player. These amounts are then modified to 3 and 4, respectively.

Chandra's Pyrohelix will deal 4 damage total (2 to each target) because it's damage to each target is increased by 1.

While Jaya, Venerated Firemage has a ruling that supports this claim, I prefer the ruling on Pyromancer's Swath (which has a similar ability) for its brevity:

If damage is being dealt to multiple creatures and/or players at the same time, the damage being dealt to each one is increased

To explain why this is the ruling, the important thing is how Jaya's ability works. Jaya's ability, as indicated by the word "instead", is a replacement effect:

614.1. Some continuous effects are replacement effects. Like prevention effects (see rule 615), replacement effects apply continuously as events happen-they aren't locked in ahead of time. Such effects watch for a particular event that would happen and completely or partially replace that event with a different event.

614.1a Effects that use the word "instead" are replacement effects. Most replacement effects use the word "instead" to indicate what events will be replaced with other events.

So now, the question is, what is it replacing? The type of event Jaya is looking for is "another red source you control would deal damage to a permanent or player". Thus, when you cast a burn spell, Jaya is not replacing the total damage your spell deals, but rather the subtotal that it deals to each creature (or player or planeswalker).

The fact that Chandra's Pyrohelix divides its damage isn't relevant to the replacement effect. That choice happened when you cast the spell, creating a spell dealing 1 damage to each of two creatures. The replacement effect, meanwhile, is happening when the spell resolves. From the perspective of the replacement effect, there is no difference between Chandra's Pyrohelix (the way you are using it here) and Dual Shot.