The way I look at it is simple: knowledge has been lost over the millenia.
Even today, people are unaware of the reason why we are in the year 2016 (almost 17). If an atheistic family tells their young child that the year is 2016, then all the child knows is that it is that year. They don't know why we started counting the years from that point, or why the term BC is used for the years prior to year 1. If no one explains it, then they will go through life under the assumption that it just is.
Say in a thousand years, the religious worship of Jesus Christ and Jehovah as deities passes into history and humanity progresses to worshiping something else as God. If they don't make adjustments to the year format and keep using the Gregorian calendar, then it is quite possible that the years would accumulate with no one fully understanding why they are now in the year 3016.
Compound that by tens of thousands of years, and you arrive in the 31st millennium during the Great Crusade.