If you attached the payment to the return, that would have eliminated the return being filed. If the check was separate, the return should have been filed. You said they asked for another return. It is common to ask for parts. Until they get all the parts, it won't be considered filed. If the IRS files a return for you, it will not have any itemizing, no cost basis, anything that would add value to your return so that you could potentially owe more.
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