Facing the same issue with the "disappearing" pets, regardless of traits (and happiness). I made a test game for checking pets. So far, no disappearances. it may be related to "no trespassing' flags - check if yours are enabled?
The only thing I noticed/been doing prior to Eco Life.
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Edit-add: Even undoing that, something isn't quite cleared with the pets so they still go off.
Families 1 (left alone no trespass) & 2 (touched trespass; left alone the 'friends' one) have no pet issues so far. Family 3, having issues with pets. And all because just turned on "no trespassing" on the friends option.
full house (sim + 7 dogs): trespassing not touched. pets poof off.
hmmm...
https://answers.ea.com/t5/The-Sims-4/ct-p/the-sims-4-en
EA_Joz