I’m sorry to hear of the missexing. Unfortunately it is common in pet shop or breeder piggies.
You will need to treat her as if she is pregnant and follow the pregnancy guides on this forum accordingly. As well as having a plan for living arrangements going forward.
https://www.theguineapigforum.co.uk/threads/pregnancy-and-nursing-diet.109377/
https://www.theguineapigforum.co.uk/threads/pregnancy-guide.109375/
It’s good you’ve separated them and they can still interact through the bars only. This will prevent loneliness.
Why is she on baytril? (I assume it’s because of the scratch?)
Antibiotics will often upset their tummies. It is advisable to use a probiotic while on antibiotics. You must also switch from lifelong, routine weekly weight checks and instead weigh her daily while she is on antibiotics. this will enable you to more closely monitor her hay intake (you can’t judge hay intake by eye). You will also need to step in and syringe feed her if she isn’t eating enough hay for herself to stop her from losing weight.
Not Eating, Weight Loss And The Importance Of Syringe Feeding Fibre
Complete Syringe Feeding Guide
Weight - Monitoring and Management
Its quite normal for piggies to not like being handled, generally they aren’t cuddly creatures but it’s not going to have anything to do with the antibiotic itself.
Two weeks is a very short period of time for them to have been with you. It can take weeks, months or sometimes years for them to settle. It’s best to pick them up by herding into a carrier first and then picking up from the carrier. As prey animals, picking them up is scary and most won’t ever like it. Some will eventually like a cuddle (but still won’t like the being picked up part), but not all of them.
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