Taxpayer has two business as LLCs. One is taxpayer owned it as SMLLC (this year 2023 is final year). Another business is owned joint venture  by husband and wife in the community property, considered as SMLLC. 
Because the nature of tax software Professional Proseries , sche C is checked mark CA LLC , then able generate business tax form CA 568 LLC . We cannot check mark  both sche C  as CA LLC on the same Fed tax return sent to IRS
I have read the instruction how to efile one business CA LLC form 568 and make another copy return, uncheck the first sch C as LLC and check mark the second one as CA LLC and efile the second business tax form 568 for state only 
My question:
On the Fed return: only one sche C is checked mark as CA LLC, instead of both . Because the second business /sche C CA LLC is initial tax year. Should we have any issue with IRS later. Any one had its experience  and how to resolve it?
I am worried because taxpayer can have option to file as Partnership 1065 or SMLLC on sche C . Either 1065 or SMLLC  has not seen with IRS record. Only show as Sole Proprietorship
My idea: I attach the second business LLC certificate, explanation why not check mark as CA LLC on second sche C,  and the Professional Proseries instruction as pdf attachment for IRS. Is it work? 
Please any tax expert advises me . Thank in advance