Paperesso manages a printout with two separate files; one file for raw printout rendering data (currently only supports *.pdf) and another (*.paperesso) for page marking related data (ex. ink notes).
Paperesso doesn’t currently support merging these two files into one file. However, Paperesso do support printing to any printer currently installed for Windows 10. Thus when you need to merge the base printout and its ink notes into one PDF file, you can use the "Microsoft Print to PDF" printer built into Windows 10. You can also select Paperesso printer and feed them back into Paperesso as a printout.