The key to overcoming fear of re-factoring (which is a reasonable fear to have) is having a good unit test suite that you're confident in. One of the code bases I work on is pretty poorly factored, and the unit test suite is not much better. There have been one or two times where I've made what seemed like perfectly reasonable and logical refactors, only to find I'd introduced a bug elsewhere in the app. I'm now extremely cautious of the code base, and will take a very conservative approach to any change I'm making.

At some stage (since it's possible large scale changes may need to be made to this app), I plan to re-write the test suite from scratch. At the same time, I'll hopefully be allowed to refactor the code base.

I certainly wouldn't want to refactor without that safety net of the test suite. Once a code base reaches a certain level of complexity, it's impossible to keep every edge case, scenario, possibility, etc. in your head. That's why we have computers to take care of those things for us.