What 1099-MISC? I thought you didn't get one. Is this a "fake" 1099-MISC that you entered to substitute for it?
If so, then, yes, delete it, because you would hate to enter a fake 1099-MISC that disagreed with the real one that they copied to the IRS but forgot to send to you.
The important thing is that you report the income. If the IRS ever writes you about this, then you can tell them what happened. Since you reported the income, they won't have much to be upset about.
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