Part way through the transformation process of swapping the roles of humans and dogs, a fatal error had occurred within the Chronivac's processing chip, causing a catastrophic error with the transformation. Humans, or what they became, had gone to plan without a hitch. Jeff had transformed into a bipedal creature who's lack of higher thought process was clear, but still friendly and now with the inclination of breeding with females of his species. Other humans were also transformed just as Jeff had intended. Every human was bipedal and were essentially now filling the role of dogs. That side of the plan went as planned.
The fatal error occurred with the dogs. The Chronivac blue screened at the point when it was transforming the digs, and due to a corruption of the process, dogs got deleted from reality. Dogs failed to be transformed properly and were accidentally removed from existence, all because an unfortunate error had occurred part way through. This should've meant that there wasn't an intelligent race anymore since humans were now as smart as the old dogs were, and dogs were deleted, however the Chronivac had a backup.
In the event that a change or error results in no more intelligent races left on earth, the Chronivac would do a 'factory reset' of earth. This means that a race or species would be transformed to become intelligent, and the species that is transformed is the one that is treated as a 'back-up species'. Most Chronivac's treat humans as this, however Jeff's Chronivac incorrectly assigned another species as this race. Obviously quite clear now that humans would likely never go back to being the intelligent race on earth anymore.
Which species did become the back-up would be unknown until their transformation into an intelligent speices was complete. They would effectively act like old humans do and history would adjust so that whichever species did pick up the mantle, there would be no sign that humans ever ruled the planet. Paintings of historical figures would change to match the current species, and names and some features would be more akin to the old human languages and customs.
Whichever species did get transformed to become intelligent, whatever their old role was would be balanced out between humans and the new dominant species. For example, if the dominant species was now cows and bulls, humans would gain traits of providing dairy products to the dominant cows, but still also be treated as pets and as old dogs used to be. As for the dominant cows, they would still have their regular vegetarian diet and some cow like habits would remain with them.
For aquatic species, human would remain relatively as they are but the dominant species would live both land and sea with some underwater cities now existing.