Flies in Incubator, Can they Compromise Viable Eggs?

Yup, I would say 'infestation' is the word for your day today. Yuck. Come to think of it, flies can be big disease vectors. Bacteria can definitely enter through the shell. I should have thought of this before. UGH, how much longer is your incubation? I have no clue about goose eggs, so forgive me. You are going to have to eggtopsy those disgusting eggs. Do it in a ziploc bag and look at the contents and see if you can tell if there was bacterial infection in there. You might see green or kind of neon yellow nasty goo.
I'll have to finish my dinner then before I start cracking, haha! Oh boy, this will be interesting. The goose eggs have a couple more weeks to go, but I have 4 weeks of staggered hatches in there so some eggs have only just started.
 
Do you have an other incubator that you could move the viable eggs to? I would spray them with some sort of egg sanitizer (yeah, I know that's a no-no) and move the eggs out of that bator, and set them up in a new bator. I would then vacume it out, and completely wipe it down inside and out with a good bleach and soap solution. Does it have a fan? If so, I would turn the fan on, and completely wrap the bator in plastic. Leave a bowl of strong bleach solution in the bator. Let the fan run for 8 hours or so. I suggest that you do this outside your home.

Those flies are a cess pool of bacteria. I am surprised that you have any eggs that hatch at all. Any chicks that do hatch are going to be maggot food. The flies will be attracted to the moist chicks, and will be laying eggs on the chicks. Fly eggs hatch incredibly fast. The maggots will immediately go to work devouring the chicks.

Before committing eggs to that bator again, run it for a day or two, perhaps putting something in there that would be an attractant if there happen to be any lingering flies or maggots.
I have a couple cheap styrofoam incubators, and one 'high end' forced air one, but that one has Emu eggs in it right now. I'll power up the spares now so the eggs have a place to sit while I do the clean out. Yes thankfully it has a big fan, so I'll be utilizing that for sure. I will definitely be following your cleaning suggestion!!

I did get 1 dozen of the 4 to hatch, but I honestly should have thrown them all out once the flies started. This has become such a mess, especially because of how many eggs they could have compromised.

I would not use insecticide. Bleach will do the job, and once the bator is cleaned out, will dissipate, not leaving any residue.
Lesson learned. Follow your gut. If a situation looks like it may cause harm to your flock or your equipment, refuse to get involved.
Definitely lesson learned. With over 8 dozen eggs in there right now, I truly hope the damage isn't going to be widespread. Thankfully I have only my own eggs in right now, so I did not comprise anyone elses. I will be much more careful next time I consider taking on eggs that are questionable in appearance.
 
Those are blow fly egg larvae. Their attracted to rotting flesh and in this case eggs. I would shut the bator down and disinfect with a 10% bleach solution and a spray bottle.
Wow, well I guess that makes sense then. Great eye! I'm going to let the spare incubators balance out tonight, and disinfect the main one in the early morning. I only wish I had started the process sooner.
 

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