The scribbles in the PDF files are saved as a seperate XML file on the iLiad and get displayed on the iLiad on the PDF. When you want ts "save" your scribbles in the PDF, you can use the Compagnion Software from iRex to merge the scribles int a new PDF file or even better use the community made java merger:
https://www.mobileread.com/forums/sho...=java+scribble