I do scribling different way. I have pdf files with several blank pages. Open the file, activate scribbling in text and scribble.
You can export new pdf with scribles. Also "hand notes" file assotiated with given pdf is in subfolder .Onyx (the same name and extension scatch (or something very similar) )
I even tried, that it is possible use .scatch file with another file. I started annotate with very long file (2000+ pages) and realized, it is 5 books. I decided, to split the file to separate files, one book one file, but wanted to keep my freehand annotations. And it worked!
I had 5books.pdf and scribbled in first 300 pages.
.Onyx contained 5books.pdf.scatch file
I split 5books.pdf to files book1.pdf, book2.pdf, .... (and put the files in the same folder as 5books.pdf)
I made copy of 5books.pdf.scatch and renamed it to book1.pdf.scatch