Uncheck and check a comment in your report, then go back to the HTML version. This regenerates the PDF and solves 99% of PDFs that didn't generate or update
Check for copy-pasted text that included illegal characters (often pasted in from HTML or a text editor that includes encoding when copying from it.) Look in new defects, header text or any uncommon part of the report
Check "Page break inside comments" setting. This will allow comments to be broken up by a page break to save white space. However, if a comment is to large to fit on just one page, and this setting is off, the PDF will not generate. In your Report Settings, toggle this setting if the PDF still does not generate!
Our troubleshooting with these is making a copy of the report and just deleting sections until the PDF works, since the PDF generator doesn't give us specific errors.