Hello @TommyA9 ,
True PDFs cannot be inserted in emails, except as "attached" links (click here for more details). When you upload a document, our system always creates a PNG image of the first page, if you want to use that as a preview or way to link your contacts to the full PDF. This same process occurs when you create an email from a PDF, though some additional design elements and action blocks will be automatically included in that template.
If you want the links on your PDF to work in the base email, you'll need to recreate the PDF as an actual email.
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