The help text to the "Replace All" checkbox says
Replace all servers in the Maven settings.xml file, even ones not found in the provided list of credentials
In the Config File Provider Plugin version 2.9.3 this does not seem to work. Artifacts can not be resolved from a server if its credentials have not been specified explicitly trough a credential setting.
After adding a credential for each server id everything works as expected.
Either the mechanism is broken or the help text is wrong.