The issue arose after I renamed the module file (ending with .gwt.xml) to better represent the module functionality. I also updated all relevant files in the project (search for files containing the old name to find them) accordingly.
Starting the application after that modifications ended up in an error (“[ERROR] Unable to find ‘<old module name>.gwt.xml’ on your classpath; could be a typo, or maybe you forgot to include a classpath entry for source?”) as the AppEngine tried loading the module by its old name.
Solution: Delete the launch profile for the project (by choosing “Run As…” -> “Run Configurations…” from the context menu).
Obviously the GWT does not check nor update the automatically generated launch profile thus you need to delete it to force the GWT to create a new profile from scratch taking the project changes into account. You might also adjust the profile according to the changes made, but deleting it is the safe and easy way.