The thread at Error about two different forms with same formid and version - #4 by LN provides two possible approaches to recovering from this state. Alternately, you can wait until Collect v1.29 comes out later this week. It makes some changes to how forms are deleted.
It would be helpful to learn more about how you reached this state and why you downloaded two forms with the same formId and version so that we can make sure we have addressed that case.