Zon-Kuthon is losing slightly too quickly.
Zon-Kuthon is a god; and depending on how you count it, either a very old entity, or something built out of the corpse of something that old. He models reality, therefore, entirely in probability distributions, He has no mortal heritage of any other way of seeing.
When this war began Zon-Kuthon formed a probability distribution over how long the fight should take, and seeing a chance to drag it out long enough to ruin the crops and visit misery on a generation, He gambled on that chance. But He is losing too fast, in the unreasonably far tails of that probability distribution, especially given the further information He now has about the war's participants.
The external-demigod-assembling fragments that Zon-Kuthon deliberately set to reunite with Himself quickly and early in predictable locations, to act as tests of the theory that all His longer-buried fragments are being hunted and destroyed somehow, returned to Him. And yet Zon-Kuthon, well, He does not have an ominous intuition, He was never that mortal. He has rather the hypothesis that Nethys is opposing Him, that this is the reason for His losing too quickly, and that His longer-buried external-demigod-assembling fragments will be gone, if so.
He randomizes, then, and based on the result makes an expensive calculation of where something will be while its trajectory is complicated; He focuses much of Himself someplace it is not all convenient for Him to be, losing ground in the war as He does; and there He finds that His external-demigod-assembling fragment that should have been flitting through that location is gone.
He knows, then, He understands the betrayal and that Nethys it was who worked it all upon Him from the beginning.