Sky, I might be wrong about this but I think the flies are only (or mostly?) attracted to bad eggs to begin with...even if we can't smell them, flies can...it's their "job".
But yes, their maggots will mess up the rest, so this is why I take great pains with clutches of eggs laid to separate them as soon as I get my hands on them...so I can easily toss out the ones that go bad- that way the good eggs are safer.
It takes patience to separate eggs (that's an understatement!): the sooner you do this after they're laid, the easier it is because the eggs are softer & still moist...but it CAN be done even when dry. Always maintain them in the vertical orientation as laid...no turning. (I know you know that) If in a big clump, easier to subdivide them first if you can. Then I take just a drip of water from fingertip (or use an eyedropper) & place it where 2 eggs are stuck together to re-moisten them. You must not get the whole eggs wet or they can drown. Once that contact spot is moist, I gently roll the eggs (one in each hand) slightly towards, then slightly away, back & forth, & you'll see then eggs slowly loosen up, until they come apart. Plant them in the damp vermiculite & keep working on the others. Slow & easy...yes, I've done this with big & well-adhered clutches.
You may see a slightly thinner spot on the eggs where you've separated them, but as long as you don't pull them apart to where they open, they are still fine & can go the distance, & hatch just fine. Too much humidity can drown the eggs...it can condense & drip on them. Anyway, good luck!I hope at least some hatch for you, it's so much FUN to watch snakes hatch out!
BTW, did you candle them? Do you know about that? How to tell the good eggs?