Using bibtool with biblatex

Maybe this does not directly address your question but as you are already using biblatex, biber might be an alternative to bibtool as outlined by this answer: https://tex.stackexchange.com/a/145168/84655

If test.tex is your latex document, just run

biber test --output_format bibtex

and you get a file called test_biber.bib with the entries referenced in test.tex.

I found an answer to this. Change \bibstyle to plain in your .aux file, and delete the \citation{biblatex-control} line. Also delete test-blx.bib from the \bibdata line. bibtool should now be able to read your bibliography as per usual.