Check is equivalent to cash. Do you have other self-employment income to report? if not, the amount showing on your Schedule C will match the 1099-NEC if the company did file one with the IRS. I don't see any issue down the road.
As long as you report your income, there is nothing to be afraid of. IRS wants us to pay the correct amount of tax, not a penny more. The company should send you a 1099-NEC if it did issue you one.
Did you work for the company in prior years? If so, maybe you can find out the EIN from a prior year's tax form.
@TheWisdom
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