"It's not clear what you are doing."
Ah, sorry.
The main VI will be used to run instrumentation remotely. Many behind-the-scenes features of this main VI--such as the addresses of the actual devices--is hidden from view and password-protected. The intention is to prevent users from inadvertently throwing inaccuracies into the feedback or breaking the communication lines (and, in one case, to prevent damage to the devices).
The point of obfuscating the settings file is to slow down people who think that they know what's going on better than the administrators do--we don't want them to decide, "well, I think this probably needs to be changed, and I don't feel like dealing with my superiors, so I'm just going to look up the password and change stuff without telling anyone."
Someone who *really* wants to throw a monkey wrench into the process could still sit down, sort things out, and make a mess, but then (1) we've clearly got problems between chair and keyboard that need dealt with and (2) the administrators can just reinstall the program from scratch to fix things, if no simpler solution is available.
We're not worried about data loss or confidentiality at all at this point.