Can you clarify the situation?

You first said "when applying for EIN", which is usually done at IRS.gov.  But then you sake if "return will reject", which seems to imply you are preparing the tax return (not applying for an EIN).

Can you clarify what exactly you are doing?

Schedule C does not use NAICS, it uses "Principal Business Activity" codes that are listed in the Instructions (they are based NAICS, but are often more broad).