There has been a lot of good discussion here http://customsforge.com/topic/33172-remastered-messed-up-scoring/page-10?do=findComment&comment=233138, and a new patch has been generated that seems to work very well, although perhaps imperfectly. What you have observed is what I observed when I used the Custom Game Toolkit to reset mastery scores to zero. Soon after that we were advised not to use the the CGT because the code changes in Remastered made the CGT nonfunctional. I suspect that the same thing may apply to the Song Manager. If you use rstoolkit-2.7.1.0-caa41fe5 to prepare your CDLC (I went back to the EOF files, rather than importing a psarc), give the song a new version number, answer yes to the question about changing the application ID, delete your original CDLC from the DLC folder in the Rocksmith 2014 folder, and replace it with the new CDLC, you should not have any trouble. Remastered has am embedded song manager. Caution, once you start the game, you will have to create a new "bug free" profile, so for the time being your old profile(s) will not be available, but this is only until the pro's figure out how to fix everything that has been changed (I'm told this may take a while). But do go ahead with putting your CDLC back, I find it's working very well.