If she's losing weight...
If she's not eating properly...
If she's pooping less/smaller/dryer poops...
Then she's not getting enough in the top end (and the pooping runs a bit behind - maybe a day or two)
I would still be trying to supplement with the syringe although if she's eating some things I personally wouldn't be getting up in the night to do it but it would definitely be something I did in the day time. The worst that can happen is that she'll be too full to eat anything on her own but that's not usually a problem people talk about! She needs nutrition and energy to fight off her disease. It gives her the best chance. She might not feel like it and it might be a bit of a battle but there are ways to make things easier like wrapping in a towel (the piggy burrito) and 'piggy whispering' to show you are trying to help but with love
Understanding Prey Animal Instincts, Guinea Pig Whispering And Cuddling Tips
You won't have to do it for ever but just to tide her over until her meds start to take effect and she can eat for herself.