Password protect Shimano Di2? I'm working on a bike with Shimano Di2 (electronic shifting with servo motors in the derailleurs), and I use the e-tube software on a laptop to configure it. 
What I would like to do is be able to password protect the derailleurs setup so it is not able to be changed unless the owner wants it changed. So it's not able to be changed by someone else without the owners permission.
This is an odd question. The sentiment that the only security here is physical security is correct. Think about the following:


The Shimano Di2 components are not mated/matched to a specific computer or instance of E-Tube software. So there's no 1:1 relationship.
Therefore, any computer equipped with the SM-PCE1 or SM-BCR2 programming cables can be used to modify the configuration and firmware of the Di2 componentry.
This has to be done via the junction box/charging port. 
Firmware can only be downloaded from Shimano and applied through this interface. And while the application has comprehensive logging, it's unique to the computer. There's no audit trail on the devices themselves.
Since this is the case, where or when would there be an opportunity to password-protect anything? You could protect your computer, but any computer can be used. The devices are relatively dumb, and the firmware is likely overwritten during updates.
E-tube is basically used to apply firmware and manage custom settings. You can save presets and load from a configuration file, but firmware is not revved very often.


Given all of this, use common sense. You can just keep the bike secured or limit access to the bike's junction box (think low-tech, like duct-tape or hot-glue). Or you can inspect settings and check firmware revisions. 

In the end, the Di2 junction box is the brain of the system. Someone with ill-intent (and physical access) could just replace the entire module in 30 seconds or so. You're seeking a technological solution to a people problem. 



pix!

physical junction box and proprietary port


programming interface recognition


application and communication logging


device settings


firmware revision dialog