PokéBase - Pokémon Q&A
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Good question!
What do you think?

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Desolate Land and Primordial Sea do not prevent each other from happening; they only prevent normal weather like Drizzle, Drought etc. from happening. They are active on the field as long as Primal Kyogre or Primal Groudon are active on the field.

What will happen is if both are sent out simultaneously is that the one with the slower speed will have their weather take over, i.e. if Groudon is slower than Kyogre, the animations for Primordial Sea will activate and then Desolate land will take over.

I saw a screenshot of someone using both against a Plusle and Minun, and Desolate Land was the reigning weather even though Kyogre was also on the field (I have yet to find it). EDIT: I found it (tumblr link)

This Smogon post has a FAQ on heavy weathers.

Interestingly, while the heavy weathers are not negated by Mold Breaker, they are negated by Cloud Nine.

Comic source

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+1 for dat pic
Psyduck pwns
Dat Psyduck 1+
... Awesome
it's canceled if cloud nine has been activated but if both primal pokemon are in play its the LAST pokemon to primal revert gets they're ability active and the one other thing that can prevent that effect is delta stream mega rayquaza's ability and the most common one to activate seeing as primal pokemon primal revert instantaneously but megas are activated on the first turn
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what if rayquassa and kyogre or groudon are simultaneously entered into the battle. Trainer one takes out rayquassa and trainer two takes out kyogre or groudon
Even if both Kyogre and Groudon had Primal Reversion,  Rayquaza's ability is Air Lock, which nullifies all weather effects on the battlefield when it enters battle and this cannot be prevented, even with Mold Breaker. Also, Rayquaza's Mega ability is Delta Stream, which creates Strong Winds, and that reduces super-effective type damage to flying type pokemon to normal damage, but this can be bypassed by desolate land/primordial sea, cloud nine (psyduck), and of course Air Lock.
I hope this answered your question.