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Hi Fabio,
For the newer BMW models, there is often a separate power cable for sale to supply a navigation system with power. This is a cable that contains a ground, constant plus and a switched power supply. The connection for this cable should be somewhere near the dashboard. But your BMW dealer will be able to tell you best.
If you connect the yellow wire correctly, you do not have to worry about interference. The yellow wire does not consume any power. The best way to connect it is by soldering.
I have no experience with the Thunderbox, but does the TB also need a switched power supply (trigger connection) to make it switch? If so, you can also use this trigger connection for your K6.
It appears that updating works best with a small SD card. I have not yet tested whether updating also works with a 256GB card. I do not have time for this yet due to a move. But if you succeed, I would like to hear about it. Disconnecting the battery should not cause any problems. If you have an alarm on your motorcycle, it may go off. Disable the alarm first. You may need to reset the time/date.
Good luck with your installation of the K6. If you have installed it, show us some pictures.