Bryan thinks about all the possible ways he can use the Chronivac, be it on the zoo animals or humans. He plans to use the Perception of Reality option so that no one will panic or get hurt. What he ultimately decides to do is swap the roles of the humans visiting and the animals who lived in the zoo. And with the filter on, no one affected would notice the difference.
He programmed the machine to not only swap roles...but to ensure after a period of time they'd return so he'd be able to fix things. Animals would become anthropomorphic versions of themselves and the humans would become animalized versions of themselves...so it wouldn't be an exact swap.
Finishing his configuration, he set things in motion. When someone new entered the zoo, at some point during their visit, completely at random, they would encounter the animal they would swap with. He imagined, by the end of a day, the zoo's residents would be former visitors.
Of course, it was still early...even some of the employees hadn't arrived yet. But the zoo was opening shortly.