Currently, I am working on a program that converts an html page into a PDF using the iText Library.
The Checker that I am using is PAC3 -->PDF Accessibility Checker
You did not specify whether you using old code (XMLWorker, HTMLWorker) or new iText code (pdfHTML).
This of course impacts the proposed solution.
In my answer I am going to assume you are using pdfHTML
There are several options:
IElement objects, and edit those, setting properties where neededTagWorker that handles all instances of a specific tag, and write custom logic to deal with the missing annotations.An example of a custom tag worker can be found here: https://developers.itextpdf.com/content/itext-7-examples/converting-html-pdf/pdfhtml-custom-tagworker-example