I'm having the same issue. I filed both my Federal and Indiana State together. My federal was accepted and I have already received the refund. My state was rejected. TT still says BOTH are PENDING, so I can't file my state return. I removed the state information. Resaved. Shut down and reopened TT. I re-entered my state info, but it will not let me e-file anything, as TT says I have already filed everything and there is nothing to file. Clearly, TT is wanting to do away with this "self-filing" and force everyone to use the more expensive "Get an Expert to do it for you." I decided to just print the taxes and mail them in.
