I think you mean you filed and an amended return to include pension income not entered on the original return, but the income was not entered on the amended return in error. So, the state will receive the amended return and copy of the form 1099-R, but determine it was not entered on the amended return.
If so, they will probably not enter the missing income, as it is your responsibility to prepare the tax return. I suggest you wait a month or so to see if you hear from the state tax department, then submit another amended return with an explanation attached as to what happened.
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