With the separate emitters, you applied a 40k watts emitter to each one, which is an incredibly strong emitter

With this much power, the optimizations in Maxwell won't work very well and that's why you see the sunlight later in the render. Best is to keep the emitter strength to normal values. With V2, if you use the same emitter material for all those separate emitters, you'll only get one ML slider which saves you memory, so it's no longer necessary to merge geometry first. If you did merge the geometry then you would have to multiply the emitter strengh by the number of emitters you merged. But in your case, this is not necessary.
If the emitters look too weak with a normal emitter value, then that's how strong they will look compared to the amount of light coming from a bright sun lit environment. So it's best to keep this balance to a natural level both in terms of realism and render time.
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