Balance Sheet Certification (BSC) currently supports one company code at the moment. There is no option to use multiple company codes.
To be able to use multiple company codes with BSC
The workaround would be to decouple the company code needed for the certification from the list of company codes needed for line item selection. To do this, use the existing BSC chain parameter for the company code to hold one "leading" company code and introduce another parameter on the BSC chain level to hold a list of company codes. The second parameter needs to be mapped to the company code parameters of the jobs in the Retrieve step to retrieve line items and balances.
This will be fixed in the future version of RunMyFinance