It’s probably what you are not missing, the latest WA update.
If your updater deletes the old addon folder and installs a new pristine one (from Curse or wherever), your custom additions are sent to the great bit bucket in the sky.
If WA allows it, create your own folder under _xxx_\Interface\AddOns (where xxx is the game version) and place your files there. Reference them in WA with Interface\AddOns\[your folder]\[filename].ogg
These should be preserved between updates.