Well, normally if you use CFW in Emunand, you only make changes to Emunand.
I'm guessing you were used to making changes in Emunand and seeing them actually change stuff in Sysnand. That observation is a bug, not a feature.
The way I described in the past is something like 'think of your Emunand and Sysnand as separate profiles. They were meant to be separate. However, both your Emunand and Sysnand profiles were sync'd, so the changes carried over. Somehow or rather, maybe a game update or FW update, caused the Emunand and Sysnand profile to now desync, hence the changes no longer carrying over'.
So either launch CFW in Sysnand, or recreate your Emunand based on current Sysnand.
All at your own risk, of course :3