When you view a saved game that is in the new format (LSV), MooseEdit will extract all files from it. This includes meta.lsb. You can swap the meta.lsb for another at this point, or modify the meta.lsb file using the "Dev" tab in MooseEdit.
I was in the same situation as Aiden, and tried this solution. I managed to edit my save file and the mod seems to be working just fine, but now when I load the save it says "warning! The savegame has detected tampering or corruption.". What I did was open the files in mooseEdit, "extract all from lsv" on a save with the mod I want and my current save, and then copy pasted the meta.lsb file over. Did I do it wrong or is the error message supposed to appear when you do it correctly?
Sorry if this is something obvious and thanks for the great editing program.