Process of elimination.
First step is a professional bike fit. If you can, get an expensive, thorough one. A lot of bike shops can throw a good fit together on the cheap, but a lot of them can't.
I don't think this happened by accident. Likely she changed bikes because she wasn't comfy, and now she is. The more upright position is likely costing a minute or two.
No one has mentioned tires, and the ones she has now may be fine. But google up the rolling resistance of tires and see if you can't get her better. When I say that, I don't mean narrow.
Another thing I'd suggest is coming up with some other rides. One ride?? I'd go nuts. How about a long, leisurely ride on weekends? That's a form of base training, and could bring her speed up.
One last thought is the saddle. I'm a big fan of Selle Anatomica saddles because they move with you. The speed difference is prob trivial, but I feel faster.
Lastly, patience. She may have simply found her groove. That can change with time. I have the same situation with my wife. I have to do rides without her occasionally.