@ton It is always interesting to see the workflows of other people. (I know, I should really write a post about mine).
This caught my eye, since I ran into the same issue:
Until last week’s Zotero update I could easily grab those highlights and notes using a plugin and save them in markdown into my Obsidian notes vault. The update broke the plugin, so that flow is temporarily out of order.
I assume you're talking about the ZotFile plugin.
One of the reasons the latest Zotero update broke the plugin is because Zotero has not a built-in feature to extract annotations from a PDF file. You can access this function from the Notes sidebar in the built-in PDF reader. Just click on the
+ button next to Item Notes and select “Add Item Note from Annotations”.