Just to chime in as I'm recently dealing with exactly this issue, although it is only occurring on one cylinder.
I recently tried to start up my car and noticed the idle was really rough. Sure enough I ended up getting a CEL. I checked the codes and it just looked to be a mis-fire in my first cylinder. I had recently had my spark plugs replaced by the dealership, so I really didn't think that the issue was with them. To see if I could fix the issue I threw new coils in (I did this on all cylinders just to be safe). After this not fixing the problem I brought it into the shop and the promptly let me know that my plug in my first cylinder was really fouled. So, the replaced the plug and sure enough everything looked good.
This continued for roughly 2 weeks until the issue arose again. So, I checked the plug in the cylinder and sure enough it was fouled up again, which indicated to me that something bigger was going on. Since I had the dealership replace the plug and tell me everything was good I decided to bring it back in to them. They let me know that the issue actually looked to be due to a leaking injector. Thankfully the injectors for my car were under extended warranty so they went ahead and replaced the injector. But, I got a call from them the next business day letting me know that the issue was not in fact resolved by the injector replacement and they found that my cylinder wall had been scored by the excessive fuel present, and the only solution was to drop a new engine in the car. Thankfully, though, they said that the end result was caused by the injector and due to it being under extended warranty I would likely be covered.
Naturally the problem didn't end there haha.. I had performed a stage I tune on the vehicle with a APR chip, effectively voiding any warranty or extended warranty on the vehicle. Because of this they blamed the leaking injector on the APR tune and told me they would not be covering the engine or any of the work done when replacing the injector. I had major problems with this because I towed the car in immediately after the CEL came on and trusted that the dealership would correctly solve the issue. But by only applying a band-aid fix to the problem I continued to drive for two weeks on a bad injector which absolutely could have been what pushed the cylinder over the edge. I personally wouldn't have a major problem with this if the issue only resulted in an issue taking $200-300 to fix. But an engine replacement is not that :/
So now I am fighting really hard with AoA and the dealership to get some level of partial warranty coverage, unless they can prove to me that the tune caused the issue. Obviously I'm certain that the tune did not cause a leaking injector, and also less inclined to believe so when Audi released an extended warranty on the part for the same exact problem.
To wrap all of that up I would push them as hard as possible to find the true root of the problem ASAP, to avoid being $10k+ in the hole.
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