The new version is removing the SCP universe integration, so I assume the subplot with the ghosts (a crossover with another SCP story during serialization) will be changed.
It's important because SCP is important, i.e. it borrows its greatness from the success of the normal day-to-day SCP operations.
Without it, it's just a story about amnesia at a government facility, and those kind of books are a dime a dozen.