Coccidia can definitely cause retarded growth rate. Now that it's been treated, you should start seeing more normal growth and weight gain. Though as your rabbit matures, she may end up being on the smaller end of the scale for a flemish, or she could catch up and be a normal size. Just no way to know for sure.
If she's not eating much hay, she definitely needs to be getting more pellets until you get that sorted out. And 1/2 cup per day for a growing flemish, is definitely not too much. In fact it might not be enough. She either needs to be getting more pellets or a semi leafy higher protein grass hay(as opposed to a more coarse grass hay),that she is actually consuming well. Or that could be supplemented with some good quality alfalfa/lucerne hay. She just needs enough protein in her diet for good growth. So either more pellets, or a leafy grass hay, or a combination of grass hay and lucerne.
Pellet amounts for a growing flemish can be much higher, and flemish take longer to grow than smaller breeds. At least the first year of their life they need a higher protein diet. So for hay amounts you're aiming for a rabbit eating a pile of grass hay the size of their body per day minimum, with healthy looking and sized fecal balls. Then for growing young rabbits the rest of the time they can have pellets, if you opt for feeding more pellets as opposed to more of a leafy grass hay(or some lucerne added to the grass hay). You just have to be feeding enough protein, from either a leafy grass hay, or some lucerne added, or an increase of pellets. After 15 months lucerne needs to be transitioned out. Though also if there are any signs of thickened creamy or sludgy urine, then lucerne shouldn't be fed.
https://rabbitsindoors.weebly.com/feeding.html
Until you can sort the hay issue out where she is eating a pile of semi leafy grass hay, the size of her body per day minimum, I would either increase the pellet amount or add in some lucerne hay. Because insufficient food, fiber, protein and calories, will definitely stunt her growth and could risk a gut slowdown and GI stasis. I would also monitor her body condition and weight gain.
Monitoring a rabbits weight
When she was at the vet, did the vet also check her teeth? It's important to make sure that pickiness with hay isn't due to a dental issue. Also want to make sure the lack of good hay eating isn't because of the hay being off. You want good horse quality green hay with no signs of mold(black and white spots, white dust, dampness, sour or musty smell), noxious weeds, or excess dust.
Hard to tell if she is a Flemish Giant or not, she sounds pretty small for a 4 month old Flemish, but her ears certainly look big (like she'll need to grow into them)!
