(With last version of maven-assembly-plugin at this time : 3.0.0)
I had the same problem with an assembly build.
I had tow dependencies with the same properties file but with a different content (one good and the other overwritting the first with missing declarations).
The problem was that i finally had the bad configuration file replacing the other in my assembly jar.
The only cleanest solution i found to overwrite the file was to :
1 - Add the good file that i wanted to keep for the build in my project :
ex: src/main/resources/META-INF/services/myfileWhichOverwriteTheBadDependenciesRessources.xml
2 - Add a fileset with 'filtered' setted to 'true' in my assembly descriptor :
<fileSet>
<directory>${project.main.resources}/META-INF</directory>
<outputDirectory>META-INF</outputDirectory>
<filtered>true</filtered>
</fileSet>
(the 'project.main.resource' property is setted to 'src/main/resources' in my case)