Hello @Pauler ,
I can't answer your question, but maybe the following does help.
Some years ago open PDFs were a problem for me when I was using knitr and rmarkdown to create PDFs.
When I checked the PDF (with my standard PDF Viewer Acrobat Reader) and noticed an error I sometimes forgot to close the PDF and the next knit failed with an error message (I realize this differs from your case).
The viewer apparently keeps the PDF reserved.
Somewhere (???) on the internet I read that the Sumatra viewer does not keep the PDF reserved.
So I downloaded this viewer and indicated in the RStudio settings (global options | Sweave | PDF preview) that the Sumatra viewer is to be used for previewing PDFs.
My problem was solved.
However: checking my settings I clicked on the questions mark near the preview setting and this opens the following article that indicates that Sumatra now is the default PDF previewer on Windows.
So probably you have different problem or you don't use Windows.