Problem with saving scribbles.

I have a PDF file 3.1MB and made a lot of scribbles (marking and underlining text). The .sketch file in the .onyx directory is 9.1MB. When I want to merge the scribbles with the file trough the menu/annotation it starts saving it, and it goes on for about 10 minutes, but it does not generate any file. With smaller files it works well. Is there some way how to do it? Is it due to lack of memory? Any workaround?

Thank you for your help.
PV Das