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You missed the chance to appeal but it doesn't meant you cannot still amend the return or file the return (if not filed). You can request abatement of penalties if you relied on your accountant advice but the penalties will not be forgiven because your accountant didn't do his/her job you didn't follow up with your accountant. "Your accountant was suppose to take care of it" is not a valid reason.
I would suggest to find a new accountant and take care of it as soon as possible. You may not be able to stop collection immediately, which means the IRS may put a lien on property or garnish your refund, but there are always other ways.
He needs to amend his return and claim the basis on schedule D. That actually happens quiet often. People assume that because they sold something with a loss or the proceeds were reinvested, they do not need to claim anything on the tax return. But the IRS has now way of knowing what happened and will not investigate or give any credits. If the basis are not claimed on Schedule D/form 8949, the IRS assumes the entire proceeds are taxable.
It is never to late to fix it. He will most likely owe much less, if anything and the penalty will be also reduced accordingly.
Just take it to a new accountant or experienced tax professional and file 1040X. This should take care of the balance due and most likely most of the penalties. When it comes to any type of credits, deductions or basis, the taxpayer has to claim them, the IRS will not assume or calculate/look up for ways to lower your taxes.
Is there anything else I can help you with today?
Yes, he can. There's no statute of limitation for amending a return. The 90 day notice only means that now the IRS can initiate collection process, like putting a lien on a property or taking his refund. It usually take some time, several month for the IRS to garnish his wages or bank account. But I would suggest to take care of it as soon as possible.
Do you have any questions? Is there anything else I can help you with today?