Thank you very much for your feedback.
Unfortunately, we do not have printers that support A3 paper size so we cannot test printing to A3. However, printing problems are almost always related to how well Java supports a specific printer model. In other words, even if we had an A3 printer, we would probably not be able to reproduce the problem unless we had the exact same printer model. :-(
I actuall do not think that printing to A3 does not work in general, because we have received feedback from other yEd users that were able to successfully print to A3 in the past.
That said, in Java versions 9, 10, 11, and 12 printing does not work as well as in the old version 8. So, if you are running yEd on one of the newer Java versions (you can check in "Help" -> "About"), running yEd on Java 8 might actually help with printing. A yEd installer with embedded Java 8 is available from the yEd download page.
Finally I would like to mention that
the file format that is produced when you "print to file" depends on your printer driver and your operating system. This is not something determined by yEd at all.
you can directly export diagrams to PDF through "File" -> "Export" by choosing the PDF format in the "Files of Type" dropdown list of the export file chooser dialog. No need to "print to file" for that.