I don’t know if this helps at all, as I only have a few Fuji RAF files in my collection from a few years ago. However, it may point to something.
The cameras I owned were the old EXR sensor models, and from those I understand that Fuji likes to use wacky designs of sensor. I know these have been a continuous cause of headaches for me finding software that can deal with them. The only ones that ever did were the Fuji proprietary software, and Lightroom.
As I understood, they used a strange diagonal hexagonal (it might have been octagonal, I can’t quite remember now) array. It was also possible to take shots that split the sensor arrays into two separate images, that were later ‘stacked’ to create an enhanced image. There were a couple of options, the most common was for low light, where it stacked a pair of under/over exposed images (the data was hidden inside the RAF file), and merged them (either in the camera, or using the Fuji software) to reduce noise. Or you could just shoot with the whole array for full resolution.
I did find out that some softwares could open and edit the RAF files, but only partially. They would only work with one of the hidden versions, which was usually the underexposed version. Converting to DNG enabled more software to be able to open them such as Photos, but the editing was starting from the underexposed version, and often ended up being grainy, and difficult to get the best out of, and are half resolution (the Fuji software maintained full resolution).
I’m currently actually working on these in Nitro myself, and still see this issue. Although on the ones I’ve started on Nitro has occasionally opened the over exposed version instead. However, when returning to those later, it re-rendered them using the underexposed version, so I had to re-adjust them. That seems to have stuck now.
I believe Fuji abandoned the EXR technology some time ago, but I didn’t know if they’d produced something similar instead.
Anyway, I don’t know if that may explain what’s happening here or not, worth a try :-).
(PS. I never bothered you with this in support, as I realise these are pretty tricky to handle, and not worth the effort for a handful of less popular, and unsupported, cameras in Apple Raw).
