After you file

I just did the same. The original return and the amended return has all the details same including the refund amount. My portion of income from NJ was $1701 and there was $27 tax withheld in W2. I paid estimated tax of $1000. In my original return the tax calculated was $80 and I got a refund of $947 ( 1000+27-80).  Now I am amending my federal return to include a K-1 form as I received it after I filed my return. It is not changing my Fed tax amount ($0 owe or refund). As part of the process, I am also trying to file amended NJ tax return (Non resident) and it is giving me again a refund of $947. The amended return should have given me $0 instead of $947. 

It is noteworthy to mention that I have e-filed both Fed and NJ return and they were processed and I got my refunds credited to my account.

I am not sure what to do here and how to fix the problem.