Multiple endings for a game prohibit having the plotline continue in a sequel with the same characters. You can have the same characters in a new plot, or the same plot with a long enough time delay to make the previous endings irrelevant. To continue the same story there would need to be multiple beginnings for the sequel, which all converge into the same plotline fairly quickly (or you would basically be writing multiple games). If you can have a sequel with various history books and plot line summaries in conversations, etc, and just gloss over the previous game's multiple endings, then there couldn't have been much difference between them, in which case there isn't much point in having them.
