Some errors are flagged for your attention and some require correcting the return. In this instance the bond premium is a deduction and the IRS does not have a problem with you not taking a deduction that you are entitled to. Leaving the bond premium off your tax return should not cause any issues at all.
I just read @rjmswarren 's extraordinarily well written essay. That is the best advice - if you have a 1099-INT and a separate 1099-OID then you should combine them in order to take advantage of the deduction that you're entitled to.
@PN10
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