Need assistance identifying a Java class or alternative solution to modify PDF print options.

In the NYSLRS project, we use print and hardcopy correspondences extensively to communicate updates to our users. For this purpose, the NYSLRS team uses the CRM Correspondence Management system. We also use a custom program that merges individual correspondence PDFs into a single file for printing. This process relies on delivered code to perform the PDF merging, and it is currently working as expected.
However, during the printing process, we are experiencing issues where some merged PDFs cause printer errors. These appear to be related to PDF annotations or formatting elements within the documents.
To address this, we are looking to flatten the PDFs before sending them to the printer, so that any annotations or formatting layers are removed and the file becomes static.