The idea that they were replaced before or during the Zoican War on Verghast doesn't make sense to me for a couple of major reasons.
The first is that, if they are infiltrators, they're a child and a baby at this point and can't meaningfully participate in the conflict. They would have a role to play in a longer war, but Asphodel isn't planning on a long war. He has a plan that (so far as he knows) will completely level Vervunhive in about two months. If he had any inkling that this plan wouldn't work and he'd need a backup, he wouldn't have personally accompanied the Spike. As it was, because he and his propaganda broadcasts were cut short, his troops were routed.
Another problem is the chain of custody: except for a few brief encounters towards the end of the book, Tona Criid spends all of Necropolis from the very first chapter with Dalin and Yoncy. If there was a switch during the book, it would have to be at the climax, while Asphodel is at the cusp of victory - hardly the time to be worrying about infiltrating the enemy. He is clearly set on a plan of annihilation; his troops even encircled Vervunhive to gun down refugees on the north bank of the river. If he wanted to infiltrate other Imperial cities, he would've inveigled his infiltrators among those refugees and allowed them to escape.
It's worth remembering too that Asphodel didn't need infiltrators, because he'd brought High Master Salvator Sondar under his sway. Why bother to sneak in a few fake grunts when you've already got the boss?
It's possible that another Chaos warlord placed them in Vervunhive before the beginning of the book, not knowing about what would happen. (Or perhaps knowing, and knowing they would survive - but if Chaos is providing that level of foreknowledge, why did any of the Salvation's Reach mission happen? To say nothing of the events of Traitor General, or the trap in Sabbat Martyr.) The question then becomes, why them? The Koleas were no one special; they didn't even live in Vervunhive. If Chaos could work such a perfect changeling ruse, why not on someone whose children would grow up to be important, such as a noble family?
Another counterargument is that throughout the series, various Chaos forces have proven very adept at infiltration and subversion on short notice. In First and Only, a trooper named Adare is cut by a Chaos artifact and within minutes has become a shambling horror made of bones. In Sabbat Martyr, Pater Sin takes control of Lijah Cuu with no forewarning or preparation (although it does take a very specific type of mind to do so). And of course, in Salvation's Reach Sirkle kills and replaces a bandsman more or less effortlessly. It wouldn't have been difficult for the woe machines to do the same to the real Dalin and Yoncy at pretty much any point.
Finally, as Greg E Uke points out in comments on another answer, in The Armor of Contempt Dalin goes through Guard basic training and is (as I recall) injured in combat on Gereon, which entails a number of scenes from his point of view. At no point is there the slightest hint that he is in any way, physically or mentally, anything other than a normal human. He has normal human limits to his abilities, he bleeds normally, etc.
Edit: As for when the woe machines were placed in the regiment, I would suggest that it's relatively recently: well after Gaunt was established as a prominent figure in the Crusade and probably after the mission to Salvation's Reach. More specific than that it may not be possible to pin down.
My thinking here is twofold: first, if Gaunt and the Tanith are already a noteworthy thorn in the side of Chaos, it removes the need for Sek to have predicted that they (out of all the thousands of Guard units in the crusade) would become important later. Second, I feel that if the woe machines were active during the Salvation's Reach mission, they would have interfered somehow, perhaps during Sirkle's assassination attempt.