We recently upgraded a 1.2 Magento site to 1.4, and shortly after the client wrote us to say that when they run order reports, no orders prior to the upgrade show up in the report. At first, I wondered if there was a crucial thing that had been upgraded that didn’t cause the older orders to work any longer (like perhaps the orders tables converting to flat tables?).
Turns out the answer was quite simple, and nothing is broken at all. If you find yourself in a similar situation, just login to your admin, and go to Reports >> Refresh Statistics. There you will be able to refresh everything, and then you will have all of your older data again. Simple!