The hob GUI asks the cooker to find hob.local.conf and will write changes to it if the cooker finds the file, however if the file exists but was not loaded by the cooker (using the -R switch) the GUI will write changes to it regardless of it not being used. This breaks the set variable/reparse model the GUI uses and needs accommodating for.
Hmmm.... I thought about storing the paths of configuration files at parse time in the cooker but because local.conf and others are loaded from bitbake.conf via include the list would be incomplete. More thought required...
http://git.yoctoproject.org/cgit/cgit.cgi/poky/commit/?id=786033f53cad2a196ae6f3a05574148578ea3894
Verify fix