Is it possible to run FOP on the server?

I'm amending my XML document on the server using ASP,

                                                   ^^^
The simplest way to use FOP from ASP is to call Java as command
line application. This involves a significant startup overhead.
Furthernmore, if your browser is IEx, you'll have to buffer the
generated PDF in order to set the content-length header correctly,
which is yet another nuisance.

I need to amend the PDF on the server in a similar fashion - by running FOP on the server or something along those lines.

I don't understand this. FOP produces PDF, it can't "amend the PDF"
in the sense it takes an existing PDF and adds some content.