The procedure for updating a mod while keeping your current save is as follows:

1.)Unpack your CURRENT save game with the OLD VERSION of the mod using MooseEdit (available on forums)
2.)Start a NEW GAME using the NEW VERSION of the mod you want to use and save it to a new file
3.)Unpack that NEW SAVE
4.)Move Meta.lsb from the NEW SAVE folder to your OLD SAVE folder, overwriting the old file

Should be good to go. You may get a message that your save has been tampered with, but that never caused me any issues.

Back everything up obviously.