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> A tool like qpdf to deconstruct a PDF to an uncompressed form is very handy.

Forgot to say this in my reply, likewise pdftk's uncompress option is my #1 stop for learning about how a PDF is built when we have issues. You can poke around and hex edit for learning too.

It is easy in an uncompressed PDF to comment out a line with % to remove objects that I think are causing issues without messing up the xref offsets. Using a fully fledged tool to edit may have side effects in how things are rewritten which ruins the point of the investigation.

Acrobat Pro has some very useful features too, but not everyone has access to that.



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