A healthy bunny can very well moult in patches and get bald spots that soon (within a week or so) get new fine velvety hair-growth on them. The bunny can look positively moth-eaten during such a heavy shed, but it’s still perfectly normal. You can also often see some dandruff during molting.
Very flaky with dandruff would make me suspect fur mites or walking dandruff. Can you feel any sort of crustiness on his skin where the dandruff comes from? Where on his body do you see the dandruff and hairloss? Fur mites are most commonly seen between the shoulderblades or in a v-shape over the shoulderblades. Here’s a link with a picture of how it typically can look:
fur mites rabbit
Selamectin, sold as Revolution (in some countries Stronghold) is very effective against mites (as the case studie says) and it’s bunny-safe. In most countries exept Australia you need a prescription from a vet. The dosage for kitten is suitable for buns. You can treat the bun empirically (without testing for mites), but if you’re not in Australia, your vet will have to decide.