Highlighting a PDF breaks it

I have a problem with some PDF documents. The moment I highlight a passage or delete highlights in DT, the PDF File get corrupted: the underlying content seems to be deleted, which means the PDF is no longer searchable and when I mark and copy a passage, I only get blank text. All annotations are empty.

This only happens when I create highlights in DevonThink. Highlights in the preview do not cause the problem. I have already destroyed numerous PDFs with this and am quite desperate now …

Is this a known problem? I found some entries here pointing in a similar direction, but it doesn’t seem to be a general problem?!

I am very happy about every hint, thanks!

I’ve never seen that problem and I highlight PDFs very frequently. This will be something the DEVONthink support folks will probably want to look at since you raise it. Might want to find some example PDF’s before and after and post here for inspection and trial by others.

That use to happen with PDF with non-standard DRM. PDF is protected and somewhat CRC-ed, when you highlight it, you modify the PDF and then the DRM inside corrupts the text and other parts. Happens same with really signed PDFs (you “sign” a contract in a PDF and the PDF is locked with your signature BMP and if it is modified in any manner except adding more signatures, it corrupts). And same with some PDF/A long term storage generated PDF.

Theoretically, DT donors DRM protection for PDFs, but if DRM is not a know and clear one, DT (and macOS, because DT uses macOS PDF infrastructure) corrupts the PDF.

Solution for that is make a new OCRed version and then annotate it. And this could be a complex thing because PDF can have set no-ocr, no-printing, no-whatever, then you need to go around that, for example, using Linux Okular PDF viewer disabling “honor” option…


I had this issues while using Catalina with PDFs originating from juris, a german legal information system. Upgrading to Big Sur fixed it for me.


@sven.luetkemeier Wow, that fixed it for me as well! Even broken PDFs have been “repaired” and all my annotations are readable again. Thanks a lot!