I ran into similar issues when trying to annotate complex PDFs directly from TeXStudio. I found that sometimes external tools handle certain tasks much more smoothly, especially for design-heavy documents. For instance, I recently tried https://www.reddit.com/r/pdf/comments/1ml57t2/using_pdf_guru_as_a_designer_loving_it_so_far_but/ and it really simplified my workflow without any of the usual headaches. It’s not perfect for everything, but it’s definitely worth checking out if you’re dealing with...
Thanks