It should just be the meta.lsb that says whether or not the save should load the specific mods or not.
If replacing the save's meta.lsb with one that has the appropriate mods doesn't work, I'm not sure what else to do. :|
Make sure that you've got all the extracted content dumped straight in the save folder and that the save you extracted isn't in that folder anymore. Only thing I can think of.
