Hi Ronald,
The company specific fields are included in the MainAccount entity. These field are handled by a method 'GenerateMainAccountLegalEntity' as you can see in the target mapping. I'm not sure if an option is missing.
Without creating a new entity for company specific fieds, you can use the MainAccount entity again and change the company before copying the data to the target.
Then the MainAccount itself will be updated (or leave these fields blank) and the data per legal entity should be imported into the correct company.