I have a similar problem that occurs when I use Zotero. Specifically, when I withdraw a pdf file from the Zotero database, then attempt to Markup in Preview.
I note there is a similarity to in my implementation of Zotero on my Mac to that described by a discussant below. Namely, that the Zotero and Evernote libraries are stored in a place named, in my case: Users/Showroom ([Me]/Library/Application Support/Firefox/Profiles/o4hrtze1.default/zotero
Here is the Error Report I filed on the Zotero discussion Forum today:
System:
Mac OS Sierra 10.12.2
Zotero 4.0.29.15
1. I create a pdf in Preview.
2. I use File Info to confirm: Permissions (Me) has Read and Write, Fetching has Read, Everyone has Read.
3. I drag to Zotero Library.
4. I click on the Zotero pdf to open (or use Zotero View PDF, or Show File, then click to open in Preview... same result as follows occurs)
5. I attempt to use Preview to Markup the document.
6. Preview says: "The original document can't be changed, so a duplicate with your changes has been created")
7. Show Info confirms the Zotero pdf file has Permissions= (Me) has Read and Write, Fetching has Read, Everyone has Read.
8. Curiously, the pulldown file menu in the middle of Preview shows the WRONG path to the file.
I think it should show: Zotero Data Directory Location:
Users/Showroom ([Me]/Library/Application Support/Firefox/Profiles/o4hrtze1.default/zotero
... But instead, the path is to a directory to which I recently saved another pdf.
... So I am wondering if Sierra and/or Preview app has changed malevolently in some way, rather than Zotero?
I've only the problem in association with pdf files I want to annotate that are in my Zotero library. I haven't tested this exhaustively. However, if I randomly select both old and newly created pdf files from my Zotero library, the same result appears.
I'm pretty sure the problem has only become obviously apparent strongly in the last week or two. However, since I installed Sierra in September 2016, I've not been using my Zotero since this week, as I have been on an extended travel away from my base computer.
I am about to begin investigating whether this feature is more widely known in the Apple discussions. I did note that Apple is introducing a new file system in Sierra....
Mendelson, E. (2016, June 23). What MacOS Sierra’s New APFS File System Means to You. Retrieved 5 January 2017, from http://www.pcmag.com/article/345519/what-macos-sierras-new-apfs-file-system-mean s-to-you
I'll also repair permissions on my Mac disk, though I'm pretty sure I did that a week or two ago.