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Rules engines might help because if there are so many if/then rules it might be helpful to get them all in one place outside the program where users can edit them without needing to know a programming language. Also, visualization tools might be available.

You could also look at logic programming solutions (like Prolog). You can quickly modify the list of if/then statements and have it do things like look whether any combination of inputs would lead to certain outcomes, etc. It also might happen be cleaner in first order predicate logic than as procedural code (or than as object oriented code).