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Sep 28, 2016 3:17 PM in response to rjkampenby LuisVintheOC,I'm having an identical problem editing pdfs opened from Box.com. It also just began happening after the upgrade to MacOS Sierra. I tried Disk First Aid and repairs but that didn't have any effect.
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Oct 6, 2016 7:40 AM in response to rjkampenby vdubya,I had a very similar issue with El Capitan, and am experiencing it again with Sierra. The difference with me is that it doesn't seem to be isolated to Evernote files. I do have trouble saving files from Skitch (owned by Evernote) that I am working on in Preview though, but I also have trouble with screenshots (.png files) that I open in Preview. During annotation I get a bubble message saying that the file could not be autosaved. If I try to save the file it won't save either.
With me the files are (usually) located on the Desktop which I do have write permissions to. I can also open the same files in PDFpenPro and save them out as PDFs. The issue for me doesn't seem to be very consistent either. While editing this comment I went back and was able to open two PNG screenshots (which I got the error message on before) and was able to add an annotation to each and save out from Preview.
Like I said, the problem for me was there when El Capitan came out also. I did all of the "voodoo-chicken-dance" things like repair permissions and other maintenance things using Onyx. I think I deleted Preview's preferences file as well. Can't remember what fixed it which of course is driving me a little crazy now that I'm seeing the issue again.
Just wanted to throw in my experience. Hope a fix is found soon.