I had a closer look at the photos and I think I know what's going on.
When you look at a healthy squirrel paw, the claws are curved and usually point slightly downward, so they can hook into tree bark etc. But when you look at her toes with new nails growing out, the old ones points upwards instead of slightly downwards.
I think this squirrel hurt its nails, maybe in a fight, maybe the paw got stuck in a bird feeder or whatnot, and the original nails broke off the bones inside the toes and now point upwards, while new nails are growing back in the position where they are supposed to be.
The same happens to us when we lift a nail and it breaks out of the nail bed, a new one will grow below the old one.
The main issue I'm seeing, is an infection going on once the new nails started to poke through the skin, followed by the inflammation and swelling.
I can imagine that she is lethargic due to pain and the inflammation.
In general terms I think she should be treated with steroids, painkiller and an antibiotic. Do you have a vet in your area that will treat her and not put her down? Others will jump in with human steroids and antibiotic suggestions.