No, you should not amend any prior year returns to remove that income. The under fair market rent is still treated as income to you and it is reported on your tax return as income.
The only difference when you are charging under fair market rent is that you cannot deduct expenses other than mortgage interest or property taxes. You cannot depreciate the property or deduct the cost of repairs or improvements.
To learn more, take a look at IRS Publication 527.
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