[yokos]

I can reconstruct your problem. You can see scribblings which belong not to your pdf file copy.
All scribbling before embedding are saved in a SQLite database. Please don't mess up your files with using SD cards and then remove them and so on.

I found this solution. After first opening of a copy file you can delete all scribblings that you see from other files this way:
(TOC/scribbles/check box to select all scribbles on all pages and delete.)
After this you can start your scribbling, because pdf file isn't connected anymore to others.

I hope this helps.

Edit: I thought that it does work. Now it is all mixed up. I can't help you.