Generated class files removed from build directory on run

I am using an annotation processor to generate some source files in a Java Web Netbeans project. These files are correctly saved to the generated-sources/ap-source-output directory, and if I do a clean build, they are compiled correctly and placed in the web/WEB-INF/classes directory.

However, if I then just try to "run" the project, it removes some (but not all) of these generated class files. Additionally, it adds a couple of ".rapt" files with names corresponding to some of the class files. These files seem to list some (but not all) of the .class files that were removed.

Any idea what is going on here? Or how I can prevent "Run" from removing these classes?

You can see from the screenshots here that the TextWebServerServlet.class and TestExternalizableImpl.class files are included in WEB-INF/classes in a clean build but are removed when "Run" is selected. The TestExternalizable.rapt and TestWebServer.rapt files are added when "Run" is selected.