The midi firmware and audio firmware are separated on all VCI-400s. This means that any audio firmware update (e.g., the standalone mixer firmware) can be updated on VCI-400s or VCI-400SEs with no issue or impact to the MIDI firmware.
NOTE: The Mac firmware update tool is no longer compatible with the latest versions of OS X so in order to update your firmware you'll need access to a PC. If you want to revert to the old firmware use the "vci400_d006.bin" firmware file included in the download link below.