To echo the cross-posting comment above. However, I see this was posted to Stack Overflow a couple of weeks ago, but with no response.
It might help to better understand the ultimate goal, as this feels a bit like you've outlined a goal constrained by the technical path you've gone down, but that your underlying goal may be approached by an entirely different and simpler way.
I would approach this with a simple R Markdown page break. Or if you really wanted to start with two distinct PDF files and then combine then, I'd rely on the R package pdftools and pdf_combine.
Any issues with those approaches?