There exists an evolution plug-in for user defined email headers. It's
part of the evolution-plugins package, at least on the old ubuntu 10.04
version that I still use. Should still be available, though, and may
achieve what you need.
Another idea that comes to my mind, is to use message filters to for
incoming and outgoing messages.
You may also go after the "Message-Id" and "References" headers. The
first of which is included in messages, at least those sent from
evolution.