I have this type of issue professionally too, even though we don't use paper. For regulatory reasons, the only approved format we are allowed to use for long term archiving is PDF/A. No attachments, only pages in a single PDF document.

It has shown to be an issue for including data, or spreadsheets. Most colleagues just print Excel files to a PDF that gets appended, but while it complies with the regulation it's basically unusable as-is.