I deleted a couple folders from my smilies manager, they do not show anymore anywhere except in gallery and links as broken. I tried to rebuild all cache. They still show as broken, correctly pointing where they used to be.
Hmm... This is a good one. Try editing a smilie through the smile manager and save it so that the cache will be updated. If that doesn't take care of things would you mind submitting a support ticket so I can have a look?
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