There should only be one entry in the file for each variable. Did you finish out CS1 more than once? It might be appending to the file instead of overwriting it, but I don't that that should be happening. Will double-check.
Edit: just double-checked and it is indeed just overwriting the file as intended. There shouldn't be any duplicated values.
As long as there aren't two with literally the same name you're good. Five and Six are theoretically subsets of Four: every time a five or a six happens, a four happens. BUT I may not have actually used that variable in CS1 and just stuck to five and six. Regardless, none of those are what determine the extra scene, they're just being tracked for fun for now.
