Well the SEP failed to meet the coverage requirements, so it's not deductible. Not being an ERISA plan I don't know that the employees have any claim for benefits. There is no provision for any offset between qualified plans and SEPs, maybe something could be negotiated with the IRS. In my experience clients and their advisors tend to let sleeping SEPs lie. Seems like a good time to repost this, I wrote it years ago (back when the 415 limit was $40K):
Ode to SEPs
At the ripe old age of 42,
My CPA said this won't do,
He told me I'm out of step,
To cut my taxes, go start a SEP.
Sent me to a TPA, he said Yep
A SEP might work, but first let's see.
Lo and behold, we have an ASG!
He told me we could work around the ASG;
But there would be attorneys fees,
Determination letters and trustees,
Not only that, I'd have to contribute for employees!
But, wait, I have no employees, they work for XYZ,
But the lawyer said the ASG
Means those employees work for me!
We'll design a plan, that will conform,
Of course you'll have to file the 5500 form.
I said OK, let's kill some trees,
But before we do, please explain the fees.
When he was done, I had to pee,
Surely I could find simplicity.
So I went online to explore
Found SEPs, 401(k)s, and more,
They needed my name and address and EIN
But had no pesky questions about 414(b), (c) or (m).
What about the IRS, would they find my SEP?
They audited my return, said I did misstep,
About my SEP they did not complain,
But disallowed my green fees, oh the pain!
My SEP grew and grew and I paid no fees
Wrote a check every year for my 40 Gs.
As for my employees, they did not know,
For their retirement, they have nothing to show.