I'm coming for a partly similar issue (don't worry, I won't hijack your thread ;) ), and the result of my experiments is that in such a case the best solution is to (a) re-install the plugin, (b) re-activate it, (c) clear the cache in the plugin's options ( wp-admin/options-general.php?page=wpsupercache&tab=contents ), and only after this, you can (e) deactivate the plugin again.
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