Google’s John Mueller said you really cannot use FAQ schema for PDF documents. John said on Twitter “It needs to be visible on the page, and reflect the primary object on the page” when he was asked if a PDF can be used.
Here is the tweet:
It needs to be visible on the page, and reflect the primary object on the page.
— 🍌 John 🍌 (@JohnMu) January 9, 2020
So if you have it displayed on the page and in a PDF, that should be fine. But the FAQ schema must reference was is on the HTML page.
Forum discussion at Twitter.