Since I have messed up my Pokemon Shuffle save, I wrote a little app for helping me to restore my corrupt save (if it happen again - I know me).
It's not the best and looks ugly as hell but it's working for me. So feel free to try. Maybe it's working for you as well.
Usage is simple: select the "old" corrupt save - select the fresh dumped "good" save - click fix. Savegame should now work after import with SaveDataManager.
P.S. Sorry for my broken english, hope you could understand what I'm trying to say
And as always: Make a backup - there is no guarantee it's 100% working.
::edit::
It seems I clicked the wrong thread for posting
http://www30.zippyshare.com/v/Po1MFWWO/file.html