I'd suggest you try to make it work for you because the artifacts you're seeing are not removable in AE. They are burned into the pixels of your footage.
Yes, and sadly I realize that this may be an unreversable effect. I was hoping there might be something available to mitigate or lessen my unfortunate byproduct.
Why did this happen?
Frequency and phase of the electricity in the lights vs. same in your camera - known as electrical shutter pumping ever since electronic cameras were invented. This would have to be adjusted on the spot while shooting, but photo cameras turned video don't provide this feature (unlike proper professional video cams *hint,hint*) so you are FUBARd. No way to correct this fully in post, put using temporal smoothing/ timewarping might alleviate some of it or give it a creative touch that will sell it...