I tried to replicate your scenario, and it seems there’s a problem with that PDF virtual printer.
I compiled a simple .tex using PdfLateX compiler:
\documentclass{article}
\usepackage{lettrine}
\usepackage{GoudyIn}
\renewcommand{\LettrineFontHook}{\GoudyInfamily{}}
\begin{document}
\Huge \lettrine{H}{ello world}
\end{document}
Then I got the output PDF with subset of the font embedded:
Then I printed that file using the PDF virtual printer:
So the embedded subset of font was removed, and now it’s substituted by a random font.
If I download Goudy Initialen Font and put it in ~/.local/share/fonts/GoudyInitialen folder then run fc-cache -fv, that file will correctly render
