I would generally recommend against trying for a major diet overhaul while there are chicks in the box. You can add stuff to their diet, but I'd be hesitant about taking away their familiar food. Finding seeds in the crop can be a problem or not a problem. I frequently find seeds in my baby parrotlets that are parent raised. In fact, sometimes for the first couple of days after I take them away for hand-feeding, I'll even find seed in their droppings. In my case, the babies are fine and healthy and have been growing well. If I were you, I'd be weighing the babies every morning. Your weights won't be super accurate because the amount of food in the crop will vary depending on how much the parents have fed them. However, if they are gaining weight every day and your seeing about a 10% increase in weight every day, then most likely the seeds are not a problem. In many cases the parents will feed softened seeds, so while it looks like the babies are getting full seeds, they are still digesting them. Its a problem if the parents are feeding the chicks a large amount of seed that has not been pre-digested at all. So in answer to if seed is bad, it depends.
Make sure to offer the parents a lot of variety and if you are concerned, supplemental hand-feeding is okay. Just make sure that your instruments are super clean because some people have found that excessively hand-feeding babies that are still in the nest makes the chicks more prone to yeast infections. If the chicks are doing poorly and you know this because they aren't gaining weight properly and/or they look dehydrated, then it might be time to pull them and hand-feed entirely.
I have a pair of amazons that simply will not feed their chicks pellets. If they don't like whatever I offered for veggies that day, they just won't feed their babies. The babies will beg and fail to gain weight and it will look as though they are being neglected. If I feed the parents what they want, suddenly they are great parents and produce healthy chicks. I feed the parents a huge overabundance of anything I think they might be willing to eat and the chicks turn out fine. My parent amazons really like frozen and thawed sweet corn, peas and sometimes they will pick at something else. Sometimes they will feed lots of seed, other times they won't touch much other than the sunflower and will hit the corn in a big way. Healthy babies every time.