I have tried on several different pets including Hati and cannot get the Essence Swapper to change my secondary pet. It stays as a dinosaur. Help plz.
To my knowledge, the essence swapper only ever worked, and was only ever intended to work, on Hati himself, and specifically the Hati that was the effect of the Legion BM artifact weapon. The version of Hati we can tame via the questchain from BfA is not the same thing. The essence swapper is effectively DOA, since the artifact version of Hati is now entirely disabled.
If you want two of the same pet, you need to tame two of that pet and place the other one in your first stable slot (and of course have the Animal Companion talent).
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Your secondary pet? The one summoned from Animal Companion comes from the first (top left) space in your stable,
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Come on Blizzard!! 
I’m sure I’m not the only Hunter out there wanting the Essence Swapper to be reactivated to its former glory.
No one wants to capture the same pets twice just for the ‘cool look’
It kind of defeats the point of having an increase in pet slots if its going to be filled with duplicates.
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I agree. Listen to your players Blizzard, for once.