The easiest way along with eschartz' suggestions is to switch your view to Collections. This view will list all your collections and you can get rid of ones you do not want from here.
As stated the first time you do this after your update is a PITA, but it should be easier to use once this step is done.
A little tip for you that I have learned the hard way. If for some reason you need to deregister your kindle device from your account, make sure your collections are fully synced with all the latest updates on a different device. Otherwise all your recent changes will not be updated when you reregister the device to your account.
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