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yes please I have the same problem, impossible to delete feeds through the backend interface.
Check if your URL looks like this /plugin/feeddiscussions/deletefeed/aHR0cDovL3BpcmF0YS5jYXQvYmxvYy8/ZmVlZD1yc3My
Note the slash. If your feed URL encoded in Base64 has some slash in it, Vanilla thinks that is another part of the URL and it doesn't belong to the whole param. So, instead of getting "aHR0cDovL3BpcmF0YS5jYXQvYmxvYy8/ZmVlZD1yc3My" (or whatever you have) it is getting only "aHR0cDovL3BpcmF0YS5jYXQvYmxvYy8", which it doesn't find in the config, as it uses the URL as key for every feed.
By the way, if you need to edit manually the config, you will find it at conf/config.php. Anyway, I think this is not a recommended way to work.
@Tim, the issues comes from function EncodeFeedKey. You need to replace or encode "/" with something else as long as you already do with "=".