There's some information in the manual as far as what makes up a modified database and how to move them. Just setting the changes in two places definitely does not do it..it is designed for one person to own their modified DB and distribute it when they wish. This was broken for you as your motivations are different - you want just replication.
Moving the entire Empire Deluxe copies the entire data collection, so that would work. It is all text, no binary files so any of the directories can be copied over. For just saved games, A copy of the saves directory might be easier (assuming the DB is already copied over). This will have the same affect as an archive, with less but more technical steps.