Apply multiple digital Signatures on PDF
Solution 1:
With FPDI you cannot edit an existing PDF document but you import the individual pages into a reusable structure. Content outside of a pages content stream (such as annotations or digital signatures) get lost.
Setasign (I'm related to that company), the authors of FPDI, also offers the SetaPDF-Signer component, which allows you to digital sign PDFs in pure PHP. The component is not free or open-source as FPDI.
See here for how to sign a PDF document several times.