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SIMPLE IRA EE and ER contributions made late; correction done and filed under VCP

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The ER discovered that EE and ER matching contributions weren't made to the company's SIMPLE IRA plan for a period of about 18 months. He immediately made arrangements to make the missing contributions including lost earnings. He filed under VCP and will be getting a compliance letter. However, the draft of the letter says that the IRS will not disqualify the plan, but it doesn't make reference to any penalties. I've determined that 4972 doesn't apply, but I'm not so sure about 4979. The IRS says 4979 penalties don't come under the scope of VCP. I want to make sure that our client covers all his bases. Should I be concerned about 4979?

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