Normal rules for early distribution applies. Unless your client was disabled or the distribution was used for allowable medical expenses, among a few other exceptions, the distribution will be subject to the 10% penalty.
The 1099-R should report NUA in Box 6. Since you haven't seen the 1099-R apparently, did you figured the NUA from the historical statements?
If NUA treatment is to be applied in a lump sum distribution (provided all the conditions under §402(e)(4) and its regulations are satisfied), the 10% penalty would only apply to the pre-tax cost basis.
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