One thing to note is that the files for 'per device' (i.e. your 00004f12e5698.cfg example) are generated from the DB. There is (at least in the case of the yealink's) a standard config file, then a template for the 'per device' config.
You can edit these files through the GUI: Advanced Menu -> Provision Editor. You'll find a list of the manufacturer (directories) on the left and files contained within those.
If you only want to change a setting on a single device, you'll need to make sure the configurable option is in the template, then edit the device in the GUI and add your settings for that device under the 'settings' area.