Fkeubler,
There are two different issues here:
1) In my postings, I conjectured that the first release of the new iOS (10.13) apparently did not supply enough power to the Lightening port to run (in series) the Audioquest Jitterbug and DragonFly Red I was using with my Etymotic Research ER-4 SR earphones. In subsequent OS updates, Apple seems to have rectified this issue since it now works for me. You can see the test steps I followed to arrive at my conclusion in my earlier posts. My guess (and it is only a guess) is that initial iterations of Apple’s software were restricting power to accessories in order to prolong the phone battery run-time: always a big-deal for mobile phone manufacturers.
2). "Legacy" devices will appear on iOS with the alert, as you noted: "This accessory is not supported by this iPhone." That’s presumably not due to your iPhone 6S itself (it’s the last version Apple supports with the new OS 10.13.x), but rather to the new OS. I’ve frequently encountered this problem with my phone when it’s plugged into a genuinely ancient Bose portable speaker, but the device continues to function properly once the warning has been displayed. Based on what I understand you to have written, that’s also your situation: a warning appears, but then the phone/DAC continue functioning, correct? If so, simply ignore it.
The fact that the DragonFly logo lights up indicates it’s receiving power through the port. The specific color indicates the DAC’s processing state (MQA, 16/44, etc).
As for the apparent degradation in sound quality, I don’t know of any reason why 10.13.x would have any bearing. As I understand the matter, the DragonFly DACs are built to bypass the (reportedly) inferior internal hardware in the phone: that’s their purpose. It’s possible (but I think it’s very unlikely since Audioquest continues to sell the Black and Red along with the new Cobalt) that there is some sort of processor/software conflict. When I called Audioquest and spoke directly to an IT rep a couple of months ago, he was unaware of any power problems and asserted their devices will perform properly with the new iOS. That didn’t seem correct (given subsequent developments) but maybe a phone call to the company might be revealing.
Having noted all that, it may be the case that your headphones themselves are drawing too much power. If the sound quality is bad now and good before, that seems like a logical conclusion.
Finally, you can test all of that by un-installing iOS 13.x and downgrading to the latest iteration of 10.12. That’s essentially the same as previous versions, but Apple updated security settings. So, it should operate for you as before, you just can’t be hacked as easily (or so Apple states).
Disclaimer: I’m not a software engineer, so take this analysis for what it’s worth (not too much)