Thanks so much for picking this series up!
I adore this series and super invested in seeing Sophia and our lovely villainess get to the bottom of this mystery and take revenge on Sophia's awful 'family'.
Also I really wonder how the prince is getting sick, is it something on the flowers? His side of the plate?
Could it be food that only effects people who have a health condition they themselves don't realise they have? (Like giving way too many sugars or carbs to someone with sugar sensitivities on a regular basis.)
We know that one of his conditions was insomnia, so it is possible that it's a lot less a health condition and possibly giving him food that makes it difficult to properly fall asleep or invigorates him. Medicine in high enough doses can turn to poison.
So possibly he was getting too much caffeine, the food had too much concentration on a specific vitamin, or as you pointed out too much sugar on someone who has a low threshold.
The first one is possible, low sleep helps cause immune deficiency and make one more susceptible to disease, the second and third are also possible since we know eating her sweets is a daily routine for him.