iText VS itext-pdfsweep-java

Are you looking for a way to render PDF's or produce them? If you want to produce PDF's, I've used https://pdfbox.apache.org/ successfully as well as https://itextpdf.com/ (potentially costs money).

So, the case study would be an optional request/collaboration, but slapping your logo on their site (as seen on their home page just below the fold) is not written as optional. Say what you will about AGPL, but if you're a paying customer, this should be an easy provision to strike from the agreement if requested. They declined and our internal legal team refused to accept the agreement as a result and so we found a different provider.

Not really a JavaFX question as JavaFX is a UI framework. Your question is therefore just related to Java. To answer that I've seen a similar feature from IText (https://itextpdf.com) or OpenPDF (https://github.com/LibrePDF/OpenPDF) as an open source alternative. Maybe take a look at those for a start and check if they provide you what you're looking for.

The behaviour you want is provided by redaction annotations. These allow you to keep working with the "full" version of the document, and apply the redactions to produce a version without the confidential information. It's a feature in the paid versions of Acrobat and Foxit's PDF viewer, but I'm not aware of any proper, open-source GUI-based tools that can handle that sort of thing. If you're willing to write some code, you can use this: https://github.com/itext/i7j-pdfsweep (it's free as long as you stick to the terms of the AGPL).