Conditioned pet Whumpee happens to be sick exactly when they are rescued from Whumper and the illness masks their conditioning from Caretaker for long enough for whumpee to get it into their head that Caretaker is their new master
Whumpee is too delirious (due to the fever) to notice that the person picking them up and carrying them away during their rescue is Caretaker and not just Whumper moving them somewhere. Of course, if they had known it wasn’t Whumper, they would have freaked out about being taken away from their master.
Whumpee seems overly affectionate/cuddly (just like how Whumper liked) and caretaker just thinks of course they want comfort! They’re sick and tired and they’ve been through a lot!
Caretaker sees that Whumpee has gotten off of their bed in the middle of the night to sleep on the ground? They must have gotten too hot on their bed because of the fever and the ground was cooler.
They won’t eat without being explicitly ordered? Whumpee is so nauseous that they don’t want to eat, but they’re willing to choke down some food for Caretaker’s peace of mind, obviously!
Whumpee is too sick to bathe by themselves, so caretaker helps them, not knowing that Whumper liked to bathe ‘their pet’ too.
Caretaker helps Whumpee out in any way (feeding, brushing hair, carrying them places, etc) not knowing that to Whumpee these are all things their ‘master’ would be doing whether they are sick or not.
And by the time Whumpee is finally better and caretaker starts to notice that all of this is still happening even though Whumpee isn’t sick anymore, they’ve accidentally completely cemented in Whumpee’s mind that Caretaker is just like Whumper. Good luck deconditioning them now!