Warning: Do a backup of your PDFs before you update to macOS Sierra

You never know what you’ve got until it’s gone.

I really love DEVONthink. Not only is it a cornerstone in my infrastructure, the company who develops it also provides useful information. A few days ago, they warned about the combination of PDFs created with Fujitsu ScanSnap and macOS Sierra:

Fujitsu warns about ScanSnap problems with macOS Sierra

Many of you are using a Fujitsu ScanSnap scanners for capturing documents. Before you jump onto the macOS Sierra train please read the following warning that Fujitsu just published:

“Problems regarding the compatibility with macOS Sierra have been found. Please do not use ScanSnap applications on macOS Sierra. Also, before upgrading your OS to macOS Sierra, please be sure to make a backup copy of the PDF files created by using ScanSnap applications. We will provide you the solution to these issues as soon as available.”

pointing to this link on the Fujitsu website.

And yeah, fuck. That’s a serious issue. The OS crippling PDFs? Destroying pages? That’s really bad news. And who knows to which PDFs it applies. Might be some older standard or a specific algorithm to create them.

So, before you update to macOS Sierra, do a backup of your PDFs. Burn them to DVDs, copy them on an external hard drive you never, ever use unless you really have to. But make sure all those PDFs, all those articles, files, etc. are safely backuped.

And seriously, Apple, WTF?


  1. Hello Daniel,
    I have, like you, digitalized all of my material in PDF format and have used Skim app for annotation.
    Since there’s an ongoing PDF compatibility issue with the OS X Sierra, have you started to use a different format other than the PDF then?
    What have you been using for annotating and storing digital notes instead of the Skim app? Iif so, what’s the process you used to migrate your digitally stored annotation to an app other then the Skim?
    Kind regards,

  2. Hoi Mio,

    I will use El Capitan for a while — and I don’t think I’m going to update my current MacBook Pro (Early 2011) to macOS Sierra. As for PDF annotations, I use GoodReader on the iPad to highlight PDFs and make notes. But then I export the highlighted text and notes via eMail. These notes end up in OmniOutliner files (one file per article/book). Formerly it was CPN, but OmniOutliner works as well (for me). So there is no need for me to save the annotated PDFs. I just keep the reduced and OCR’d PDFs (and separately, the original high quality scans).

    As for Skim and macOS Sierra — what do the forums or the developers say? Is it a problem for them?

    Judging by the Fujitsu site, it seems to be a problem with specific ways PDFs were created and there seem to be ways to reprocess the files (hopefully in an automated manner). But currently I know too little about it.

    If I were you, I’d have a look at the Skim community or ask the developers. Plus do a backup of the PDFs and monitor what happens to the PDFs.

    Best regards


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