Charl Botha has posted a handy guide to using a paper-specific bibliography file with Org mode. His use case is roughly that he wants to manage his bibliography with Zotero but wants to use Org Mode and John Kitchins org-ref package to write his papers. He also wants a small, paper-specific bibliography file that he can keep with the paper source.
That turns out to be pretty easy to do. You configure Org to use latexmk in your init.el file and add a few lines of headers to your paper source and everything works as you’d expect. Botha has a small example to show the entire process. See his post for the details.
For another take on the Org mode/Zotero workflow, see this comment by Muad Abd El Hay to a previous post of mine on Zotero workflows. It also uses org-ref but exports the entire bibliography from Zotero every time the database is changed.