Annotations aren't being recorded

I have extensive annotations (highlights and notes) on a pdf in my DT3 database. The pdf is in its own window.

When I look up the pdf in the main DT window, though, I don’t see any of the annotations. When I open it with an external app (PDFExpert), again, no annotations. Trying to save the annotations as a Markdown files yields … nothing. No file appears.

When I try to export the annotated file as a PDF (to save the annotations in case of trouble), nothing happens. The log politely but cryptically informs me that my attempt to export was “skipped.” No further explanation.

What is going on? I am reluctant to restart because I don’t want to reopen this file and find all my annotations gone. Why aren’t they “sticking” to the pdf as they normally do?


The main window should be updated after saving/deactivating the edited document window. However, there’s a known bug in the PDFkit framework of macOS when saving PDFs using the fast “Append” mode that can cause such issues (depending on the macOS version and document). This affects also but the next maintenance release of DEVONthink 3 will include a workaround.

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Thanks for explaining! Good to know this is being addressed.

FWIW I have not had this problem with any other pdf. But then this is the first one I’ve annotated since I installed Sonoma (I like to wait a long time after version X.0 before I jump in.)

The workaround I used: I used the Print option to “Save to PDF,” which created a new pdf file with the highlights. It’s not a great solution – I can’t link to individual highlights (I guess because DT doesn’t think it made them?) and I lost a couple of text notes. But it is less discouraging than seeing a completely un-annotated pdf after marking it up over a couple of hours.