change in behavior after surgery

We have 2 dogs; a female rat terrier who is about 6 years old, and a male Australian cattle dog puppy, about 4 months old. For the last few months, the two have been happily playing together every day. They got along VERY well. The terrier was still very playful, and they spent the majority of their days chasing each other, playing tug, wrestling, etc. They went on walks together and played in the dog park together as well.
   
Last week, we had our terrier's teeth cleaned at the vet. They discovered issues with one of her smaller molars and had to extract it. When we got her home, we kept the two separated so the puppy wouldn't try to play and hurt her.
   
Her recovery, unfortunately, did not go as smoothly as the vet indicated. She may have had an infection or some dry sockets that caused swelling. On top of that, she showed some behavior changes.
   
She was put on more medication, which helped, but she started spending her days hiding under the bed or couch, being afraid of everything, especially our puppy.
   
It is now a week later. We've had 2 follow-ups with the vet, and they've indicated that she shouldn't be in any pain. No swelling, no sensitivity. But she still hides all day, and she's still terrified of the puppy. If he gets close, she darts under the bed/couch and starts shaking. If there is no immediate access to a hiding spot, she tries to keep as much distance as possible and shakes like a leaf. If he gets close, she bares her teeth.
   
We're not sure what to do. It feels like we have a completely different dog...