"I filed 2020 NJ amended filing because NJ rejected my e-File due to lack of a feature at the time I e-Filed. At the time TurboTax instructed me to pay the estimated tax and file for an extension. I payed the estimated tax and send the amended return via mail."
It sounds to me that you never sent an original NJ-1040 to begin with.
You say NJ rejected your e-file, so that is what you should have mailed in, an ORIGINAL NJ-1040. However it sounds like you never sent a JN-1040, only an amended return.
That would cause an issue with the state.
They can't process an amended return if they never got an original one.
If this is your situation, let the state know you never sent an original return. More than likely you might need to start over and create an original NJ-1040 unless you saved a copy of the return that you say could not be e-filed.
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