One of the easier way to swap out locos or stock on a scenario, and without losing the scenario's existing instructions, is by using Mike's RW_Tools Utility to do this:
http://www.rstools.info/rw_tools.htmlRead the documents that come with it and on Mike's site. It takes a bit of getting used to learn how to use it, but it's a great utility that has a lot of nice features it can help one do some things much quicker and easier.
I'd suggest to make a Cloned version of the scenario first you want to edit so as not to risk messing-up the original, and also if updates are made to RailWorks or you had to do a Verify Integrity then it won't affect the edits made on the cloned version.