For any sort of eye infection the vet most likely would prescribe some form of antibiotic. As antibiotics often have the side effect of killing off alot of beneficial gut flora, it is a good ideal to add a pro-biotic to your dragon's everyday diet. Non fat unsweetened fruit yogurt, a small amount each day (half a teaspoon or less) can work, but better to buy one of the probiotics available for reptiles (or those available for human children, just reduce dosage appropriately).
Also, I suggest raising the basking temp above 95F. 95f is the minimum temperature the basking area should be and with sick recovering babies, a higher basking temp would be better. Still keep cooler areas available for them of course. The higher range (100-115F) is best.
Make sure the dragon is well hydrated, kept in as stress free an environment as possible (ie dont' handle unless it's for treatment, bath to help hydrate etc). You can also try offering easier digestable foods, such as silkworms, butterworms, pheonix worms and baby roaches. Having fresh healthy greens available helps too.
A product called parazap may also be benefial. It helps replenish benefical gut flora much like probiotics and also helps to reduce parasites in your dragon safely.
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PHLdyPayne