Do I understand you to say that you created and entered a ghost 1099-R for the excess Roth contribution removal in anticipation of the 1099-R that the Roth administrator was going to send you? Did you do that only because you did not want to wait for the administrator to send you the 1099-R?
Fortunately, since the 1099-R that you just received exactly matches the data on the ghost 1099-R, you can pretend that your ghost 1099-R came from the Roth administrator, and just ignore the "real" one.
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