I updated the firmware/software in several stages (MIB2 High) with files sold to me on eBay, all went well but I had to re-enable Mirrorlink, Carplay and Android Auto using VCDS. You must make sure that the power supply is not interrupted so battery must be in good condition and fully charged or connected to charger.
I think the standard firmware may be free but you have to look for that. Anybody also had to use VCDS tools on their standard upgrades. I know Walone did on his high unit. Thinking about it, it must be that you have the FeC license for those but you have to toggle the settings back on as Walone said. Really need. Like TMC... think you for got to mention that .
If you go to a retrofitter you draw up a piece of paper with what to check before leaving.... used Walones notes . TSR is another one to add if you have it. That one caused me grief.