Single post in Your Guide to 90%+ Breeding Pairs
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I'm not sure that the shelter does change the OT. I had two Vivillions in my daycare that I was the OT for, and they had a 49% compatibility. I switched one out for a pokemon I recieved the egg of from the shelter and as far as I can tell the OT is still the trainer who's pokemon lay the eggs. The two have a 59% compatibility, and only one of them was bred by me, but both were hatched by me.