I did vague digging around and some sort of hacking (so many years ago, I don't recall the details), and got something gross that didn't have a reference to Helvetica.
I also shelled out money to Adobe for their commercial PDF tool, and massaged the output.
Neither of these solutions were really satisfying, but they each seemed to work at various times.
Fast forward to today, and I wanted to make a notebook of hex grid paper:
I uploaded the PDF of my graph paper, and got that same error again. To be clear, the entire book was graph paper - no fonts were being used. I poked around in the PDFGen documentation (there's a user's tutorial, not so much a reference manual), and found some information that was useful for importing TTF files and embedding them, but nothing for an unused Helvetica font.
I poked around inside the source again, and discovered the initialFontName and initialFontSize arguments to the canvas object, so now, my canvas creation looks like this:
ttfFile = os.path.join('.', 'UniversalisADFStd-Regular.ttf')
pdfmetrics.registerFont(TTFont("Universalis", ttfFile))
c = canvas.Canvas("hex_book.pdf", initialFontName='Universalis', initialFontSize = 24, pagesize=pageSize)
c.setFont('Universalis', 24)
And there's no dangling use of Helvetica, and Lulu's happy, and I'm happy. Maybe this is useful to you, maybe it'll be useful to me, next time I run into this particular weirdness.