Actually we don't do much upgrading as we only install the stable release, which up until 4.1.8 was 4.0.19. Now with 4.1.8 there seem to have been some issues with the upgrade from 4.1.7, and it sounds like this may be one of them. A fresh install will never be a good option for a custom store, so upgrading is definitely the way to go. Just need to be sure to fully test the store once you do upgrade to make sure there aren't any anomalies like this one
