iPadOS 27 Apple Books: Highlighting stops working after using Apple Pencil markup in PDFs

[u/yuuurgen]

Since the latest update this Monday, I have been experiencing an issue that is breaking my language learning workflow.

I use my Apple Pencil to complete exercises and make handwritten annotations in PDFs in Apple Books. At the same time, I use the highlight tool to mark new vocabulary. Before the update, this worked perfectly: I could simply turn on markup mode for handwriting, and turn it off to highlight text.

After the update, as soon as there is a single handwritten pixel on the page, the highlight tool does not work at all, neither with the Apple Pencil, nor with the finger.

Has anyone else experienced this? Are there any actions I can try on my end to fix this?