After you file

 sometimes you will get the wrong advice from the IRS phone-call agent.

However if the IRS said your 1040 is on hold waiting for 1040-X,

you still have to assume you will get that refund and file 1040-X accordingly.

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if the IRS said your 1040 is on hold waiting for 1040-X, I'd call again and get a confirmation of that from a different agent.

 

@Angelr4560