Lets break it to separate points ignoring W2, since there is no information how W2 is related to his sole proprietorship:
1. Since you supported contribution amount with your BOY valuation, Schedule SB and the 5500 are correct to show contributions.
2. Since he had no Schedule C income, he could not deduct it.
3. So he needs to file the amended tax return that will show no contribution, which will result in additional tax with interest and possible penalties. This has nothing to do with his business account.
4. If he has personal funds to pay these additional taxes, you will not need any in-service distribution.
5. Having in-service distribution to pay taxes is the worst case scenario. The money were not deducted, but you will pay income taxes on in-service distribution.
6. And yes, any sole-proprietor should not make any DB contributions during the plan year, unless he is 200% certain, his net Schedule C income will cover the amount.