anything with XML-based FG/BGChanges will cached anew and BG/FGChanges will be added to the new cache files appropriately.
...The XML doesn't understand activating mods.
I deleted the caches and yet it didn't do anything. I even deleted all the files for stepmania, backing up the folder from application support, and then reloaded the game, turning on quirks mode after, and deleting the cache. However, the contents from application support still existed somewhere that stepmania could find, so it still had all the songs.
Now I have two problems.
1. Activating XML on charts
2. Deleting all folders for Stepmania
And if anyone else can help, remember, this is for OS X Mavericks.