Maybe your changes messed up your retroarch.cfg files. It might help if you give us your configuration for savestate_directory.

Can you run this and give us the output:
cd /opt/retropie/configs
grep -r 'savestate_directory' ./

So I found out that after doing a fresh install mupen64plus has changed where it references the game saves in a different folder being .local/share/mupen64plus/save folder. However, legend of zelda does not seem to recognize the .Sra or the .srm file I copied to that directory. Making progress, but not finished yet. Figured I'd post my findings for anyone else having issue or to see if anyone else had any suggestions.