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When modified from ACC, any component properties file will go to the config layer with the highest precedence. In case you want your changes to be written to a particular config layer then you can select that config layer also within ACC from the menu Tools -> Set Update Layer. By default the config layer at <ATG>/home/localconfig is at the highest precedence so if you don't explicitly specify any other config layer, ACC will write your changes at the component path within <ATG>/home/localconfig. Actually, <ATG>/home/localconfig has a CONFIG.properties having the property defaultForUpdates=true which makes it the default for any updates. You can change this default by changing defaultForUpdates to false in <ATG>/home/localconfig/CONFIG.properties and create a CONFIG.properties with defaultForUpdates=true within your modules' config layer so that ACC by default can write your changes at the component path in your module's config layer.
For scenarios there will not be any properties file but it would be a .sdl file which will be under the directory /atg/registry/data/scenarios/ within the config layer as mentioned above. (default is <ATG>/home/localconfig).
Properties file for targeters will go to the directory /atg/registry/RepositoryTargeters within the same config layer and for Slots it will be in the directory /atg/registry/Slots at same config layer.