Hello,
Q1: In order to use a different package you have to modify accordingly all the changeset.xml you can find in gwt-console-server.war libs i.e. in jbpm-gwt-corexxxx.jar, jbpm-gwt-graphxxxx.jar
Q2: If you want to delete stuff from guvnor delete from eclipse or webdav client. Then check in guvnor if they exist and if they don't then all good, throw a build of package to be safe :) . There is a specific situation when you get this message (i believe it's a bug) if you add an ftl file or maybe any other file that has the same name as the bpmn file. For example if you create a process test.bpmn and you set in its properties id = test and then you want to create an initial form for this process i.e. test.ftl , then forget it , you will get the message you mentioned :-/ , so this might happen with any file having same name regardless the extensions (i'm not sure haven't checked) .