Sounds like the game needs a convert function to convert a saved game to use new datafiles without going bonkers. When you load it says something like "This is being played with a different dataset then the active one. Do you wish to convert the game to this dataset?"
It would also be good if the game asked at startup which dataset I want to use based on which ones are available somewhere in the gamefolder. Since all tweakable data isn't in the data folders alone (AI's for instance) maybe some way to tell the game what files to use for a specific dataset would be good. Like dataset.txt in which all datasets are listed with names of textfiles, like mydataset.txt in which all modified files are listed and their path. Any file not listed gets to be the default file instead. I hope I made any sense there.
