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You can either refactor, or drop it.
Either way, this is what I would do first:
1. create a repository for your project;
2. import the project from the production server into a subdirectory: call it "old", "mess", or "omfg", I don't care;
3. foreach part of the code that you refactor or drop, remove it from the old directory and commit to a decent organized place.
At the end of the refactor, your old directory should be empty, but you can always go back in time and see what happened to each piece of the old system.
Regards,
life is short
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