I have not had this problem until 6/18. I play rotationally and until then had been playing with Sims on regular lots. Almost all my Sims have pets and I was not having any problems with them disappearing. Now they seem to constantly disappear. ☹️
Pets started disappearing when I began playing with a household in an SM apt. This is the first time I'd played with an SM apartment (or any apartment) since EL and the related patch. This is also the first time I've played with a household that includes a Toddler (for what it's worth).
I reset my game. Removed all mods. I'll see what happens with a vanilla test game, but I have a feeling this is one of those it's fine until it isn't problems.
Adding: After reading through the posts here, I decided to move the toddler out of her grandmother's household back to her mother's, just to see what happened. At first this seemed to help. No disappearing dogs. Traveled to the beach and a park. Came home. All seemed normal. Went to bed. Got up and tried to take one of the dogs for a walk. As soon as they reached street level my Sim reset (hair turning from grey to blonde) and both dogs disappeared.
Then I switched to a different SM household also with a dog. Of course the dog was sick, so traveled to the Vet. Dog disappeared shortly after I checked in at the vet.
Side Note: All my pets are fixed. Noticed when I took the dog to the Vet it had an option for neutering. It was no longer fixed. Huh?