qschulz:  Thanks for the explanation.

Until now I have never cared about the BBPATH variable.
Today, however, I have learned that this is very important. I have in meta-openembedded (layer-1) a recipe A with version 1.0. I have created 2 layers in one (layer-2) I have a recipe with version 2.0 and in the third layer (layer-3) I overwrite configuration files for the recipe in layer-2. 

So bbLAYERS="layer-2 layer-3 layer-1" 

Now I notice that layer-1 is overwriting the configuration file, and possibly other files. Is there anything I can do to avoid having to re-sort my layers now?