Somewhat new brewer here, but I wanted to share my experience with anyone in case it shed light on this problem. A few weeks ago I brewed a NEIPA (all grain, Wyeast 1318 London Ale III), and split it into two fermenters so I could dry hop them differently and see the result. Since I just started, I'm only brewing 1 gallon batches to get a feel for different ingredients/brewing techniques.
One fermenter was dry hopped once at day 7.
One fermenter was dry dopped twice, once at high krausen, once at day 7.
Out of the fermenter I used a auto-siphon and a spring top bottle filler. (All equipment was cleaned and sanitized with PBW and Starsan) Note that the spring filler cloged up with the NEIPA, so I had some difficulty at the beginning transferring from the fermenter to the bottles. At any rate, I filled my bottles and left about 1" of headspace, added carbonation tablets and capped the beers. I use "EZ-Cap" bottles, so I do not use the typical bottle capper. Bottles were kept in my closet, temperatures in my house did not go above 72F during conditioning.
Since I brew such a small amount, I had a little beer left over from each fermentor, so I combined them and put them in one bottle, that was a little over half full with beer. Note that this bottle was open to the atmosphere the longest, since I added beer from both fermenters. It also probably had the most yeast, since it was the "leftovers" from the end of each fermenter. More on this later...
Since I was excited to try my first NEIPA, I put the bottles of the single hopped NEIPA in the refrigerator after 10 days. I let the bottle chill 24 hours, and opened it the next day. It the beautiful golden NEIPA color that I was going for. (I would post pictures, but havent figured out how to do that yet).
On day 14, I decided to put the rest of the bottles in the refrigerator (including the half filled bottle).
On day 18 I wanted to try the bottle that had a mixture of both beers, so I opened it and the beer was very dark brown/black. It still had a slight hop aroma, but the taste was definitely off. I am not 100% how I would describe it, the bitterness had dulled, but it still tasted like beer, just one that had been sitting around too long.
This made me concerned that the other beer (the beer that was dryhopped 2x) was also ruined. On day 20 I opened the 2x dryhopped beer, and it was the perfect golden NEIPA color as well. Aroma was stronger than the 1x dryhopped beer, and was absolutely delish.
The interesting thing about this, is that I have brewed "normal" IPAs, IBU's in the 50-60 range, with aggressive dryhopping, and filled my conditioning bottle halfway, and have never had a taste/color change.
I read though the entire thread the other night when I opened up my brown beer, and tend to agree that it has something to do with the oxygen in the headspace (in my case, about 1/3 of the bottle was headspace/air) and the interaction with the hop oils and/or yeast that is in suspension in the NEIPA. In my "normal" IPA batches, I used Irish moss, and the yeast settled like a rock.
Feel free to ask questions if anything wasnt clear, just wanted to share my NEIPA experience. I have another batch that I am bottling this weekend, I will not be using my spring filler, since it was such a pain last time, and I will be filling the bottles as close to the top as possible to reduce any possibly oxidation. I will report back in a few weeks...