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open source pdf editor for linux based os?
(programming.dev)
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LibreOffice Draw can make changes to PDFs.
having layering(hope that the right word for a group of text, icons and symbols) issue where icons and symbols go missing or get replaced by square boxes
Might be an issue with fonts?
Some pdf are optimized to hell to the point of unused glyphs got removed from the embedded fonts to save spaces. When you edit them, some characters you added won't be rendered if it's missing the glyphs.
Try to make sure you have all of the fonts used by the PDF installed on your system. I tend to only make small changes, but not having the correct fonts causes issues for me.