Without performing any action, the console reports two specific errors: deny file-issue-extension and deny file-write-data. The app appears to be losing privileges to edit the document since it was changed by an external editor after the document was opened in my app. If I try to save the file in my app, it asks to duplicate the document because it has lost access to the original document
The correct behavior in a situation like this is to not overwrite the file, but to prompt the user if they want to reload the document, if so reload it and then write it.
The OS is doing the right thing by not allowing a blind write over a file that has changed.
See NSFilePresenter – (void)presentedItemDidChange to see if it changed. Reread the file and then see if you can save it. You dont say you have been denied a read on the file.
Also, since you havent posted any code it might be helpful to show what code you are using to access the file and to save it. NSDocument has built in handling for some types of file changes in the sandbox.