Where did the Extract Annotations button go?
“Extract Annotations” was a feature of the third-party ZotFile plugin. In Zotero 6, that feature has been replaced by Zotero's own advanced PDF functionality.
You can create a note from all of an item's annotations by right-clicking an item in the items list and selecting “Add Note from Annotations”, or you can open the PDF in the new built-in PDF reader and add annotations selectively. See Adding Annotations to Notes for more on the various ways of using annotations in notes in Zotero 6.
For more details on the new functionality, see the Zotero 6 announcement.