I'm still on El Capitan and can confirm that in the new 1.5 Beta of AF, the issue is no longer present. I had done some manipulations of TIFF files earlier but as it was in-between things some were done in AF1.4 and some in the 1.5 Beta. Noticed some black files in the folder afterwards but not all the ones I'd retouched. But if those black ones are opened in AF Beta and saved they appear as normal and open in preview etc fine. Think to reserve them unless you export them you have to do some modification - tiny bit of infill, notch on an adjustment curve whatever - before AF will let you reserve them as obviously otherwise it's saving something that's already there.