Since your mother and father were designated beneficiaries of your brother's 401(k), your brother's estate has no involvement in the disposition of your brother's 401(k). Nothing about it gets reported on an estate income tax return from your brother's estate or on a Schedule K-1 from your brother's estate.
And you are correct regarding your father's half. Since the inherited 401(k) was set up after your father's death there would be no designated beneficiary of this inherited 401(k) and the plan has no choice but to distribute the account to your father's estate. In that case your father's estate would file an estate income tax return (Form 1041) and generally would pass the income through on Schedules K-1 to your mother as beneficiary of your father's estate.
