I wrote a buch of messy JUnit test in my plugin and figured out, that the method

MemoryConfiguration.addDefaults(Configuration)

does set the configuration, and the previous defaults are lost. More exactly, the root entries are fine, but a child section is overridden.

The reason for that is, that the method calls

addDefaults(defaults.getValues(true));

and getValues(true) also returns the child sections, and and set them. This overrides previous child sections.