I scanned a few pages of my kid's artwork to make a multi-page PDF. Then I opened the PDF on my Mac using Preview, and did a bit of copy-pasting to clean up a few smudges, by covering them with square "patches" of the background colour that I copy-pasted on the page. I also copy-pasted my kid's name from a different Jpeg drawing they'd made, and stuck it onto this PDF.

I saved this booklet PDF with a new name... but when I open the new version, those patches still show up as moveable elements on top of the PDF - they aren't flattened down as a part of the file. Is that possible?