greetings! and help!

Boo everyone. I'm Amanda and the proud owner of two piggies Penelope and Lila. My girlfriend and I are a bit concerned about Penelope. She is two years old and was purchased before Lila who is just one. They have always been in separate cages but get plenty of floor time and really enjoy eachother.
Our concern is that Penelope started acting strange a few days ago. she was huddled in her cage on 1 side after we had cleaned it and refused to go inside her igloo. She seemed and was acting terrified all if the sudden. just very unusual, even for Neppy. :crazy: I also noticed when I moved something in the cage she screamed...also unusual. She was purchased at a pet store (never again) so she has always seemed a little more jumpy than Lila but this was out of character.
So...that night I took her with me to therapy (I know its wacky but my doc loves her) and she sat on her lap the entire time all snuggled and super squeaky. so when it was time to leave I put Penelope in the tote bag I always transport her in and as soon as I got into the car she leapt out of the bag and into my lap-this has NEVER happened! So I drove the entire way home with her on my laP. She was squeaking and content the while way home. When I tried to put her back in her cage she freaked. I took the igloo out and she still wouldn't go on that side of cage so I called the vet. The Dr asked about her eating and dining and eliminating which seemed mostly normal, though she seemed to be less interested in her pellet food (which by the way is Sunaturals organic with tons of yummy stuff that she normally cannot get enough of) but she was reading parsley, carrots and her Timothy hay. She had me check for mites on her fur and I didn't see any or signs of any. Told me to keep an eye on her for now because she was eating and drinking.
We decided to give her floor time to see how she responded. Though timid at first she was very happy to see Lila. We had noticed she wouldn't drink out if her water bottle but when we put a dish if water down she drank.
Later that night we put her to bed in her cage and for a hideaway added the straw house she lives to play with at floor time. We had to physically placer get in the house but she stayed there all night.
(sorry this is so ramble and long) the next day we snuggled her more than usual as she seemed must comfortable and happy then. We gave the girls must of the day together in floor time and even put Luisa in Penelope's cage and she was staying to act more like herself. Yesterday we gave them floor time all day in their corralled area similar to a c and c cage. And she seemed mostly herself. Eating her food drinking out of the bowl and playing.
Vet said coins be hormonal changes since after is just over two years old. We are now contemplating throwing away her cage and water bottle and creating a c and c cage for the two if them.
Any thoughts ideas or experiences similar to ours would be helpful and must comforting