Currently the data dump does not have enough information to do accurate reputation calculations. For example, if you cast a downvote on someone else's post the -1 penalty you incur is not recorded in the data dump. I think there are other issues as well, but that's the one that sticks out at the moment.
Now, there is good reason not to record the individual votes themselves, but you could aggregate it. Perhaps something like a day-by-day offset that accounts for the difference, recorded in the votes table via a new vote type and new column (OffsetScore). Of course, I haven't seen your actual schema for recording and handling these issues, and so there might be a better way to do it. But something to allow data dump queries to account for the anomalies would be nice.