Bourne isn’t running on muscle memory. He suffers from a variant of retrograde amnesia which affects his ability to remember who he is, but doesn’t affect his skills. From what I’ve read on the subject, it’s entirely possible for an amnesiac to retain basic knowledge, in isolation from specific memories. Which is to say, this can happen.
There are details about exactly how Bourne’s amnesia manifests itself that may be unrealistic. An individual can retain general knowledge, and skills, but that doesn’t mean they’re not impaired, and when you’re talking about something like tradecraft, being in full possession of your faculties is a little important.
For whatever it’s worth, the only time I’ve ever interacted with an amnesiac, they were suffering from anterograde amnesia. This is the inability to form new memories after a triggering event. (You can see this one demonstrated in Memento, if you’re wanting a point of reference.) So, I can’t really speak to how accurate Ludlum’s work was when it comes to that element.
In a 1986 interview, Ludlum claimed that he came up with the idea
for the Bourne trilogy after suffering retrograde amnesia and losing
about 12 hours. The old advice is, “write what you know,” and apparently Ludlum did, in this case.
I know I’ve recommended it before, but if you’re thinking about writing spy fiction, The Bourne Identity is a book you really should read. The 2002 adaptation is also good, but it uses the same premise to tell a very different story.
Normally, I would strongly caution writers against using
amnesia in their stories, unless they have something fairly creative
they want to do with it. This has more to do with amnesia plotlines
being run into the ground, and becoming horribly cliche over the years. Memento uses it as a jumping off point for an interesting narrative format. Bourne uses it to play around with the spy as a character archetype. Bourne also uses it to play up the traditional mystery of a character who doesn’t know who they are, or who they can trust. That’s one of the approaches you probably want to avoid.
Because amnesia works so well for establishing a blank slate, and giving the audience a point of view character who is exactly as unfamiliar with the world as they are, it’s become cliche. I fully believe there are methods to use amnesia as a useful narrative tool for your work, but a lot of the more obvious approaches have already been done to death.