userClass, baseClass, package, mainForm, and guiResource properties were all missing from the codenameone_settings.properties file. I put them back but for some reason opening the properties panel in NetBeans deleted them again.
As this project has always been a GUI project from the very start (years ago) I don't know what caused these properties to go missing.
After a few saves and putting the back a couple of times its working now and no longer getting deleted out of the properties file.