Due to MAPADOC upgrade, had to re-copy the MAS_SYSTEM, SOA and 2 company folders on the 4.05 version to the 4.05 upgrade folder for a v 2016 upgrade. During the migrate, answered yes to system files, no to VI and no to existing companies just selected the two company codes with EDI. I was under the impression that No to existing company codes would leave them intact, but now company code maintenance only shows the two newer migrated companies.