You could try starting a new game, but i'm sure they should work on existing save files, especially the hexen menu(which you would see a soulstone in the menu command list).
But since you may be experiencing some issues i'll have to ask for some screenshots in order to troubleshoot the issue:
- index.html file (open in notepad or any similar program)
- TY_ModLoader.js (open in notepad or any similar program) (i need to see the TY.MOD_LIST)
- The mods that you have inside of your "mods" folder.