I can get the same symptoms with the multimodule sample app in roo 1.2.1
Run the multimodule.roo script
Import the generated project into STS
and at some randomly chosen point STS will decide to delete the controller aspects
eg in this example it was triggered by selecting maven - update config
Welcome to Spring Roo. For assistance press CTRL+SPACE or type "hint" then hit ENTER.
roo> Deleted SRC_MAIN_JAVA\com\example\petclinic\ui\mvc\VetController_Roo_Controller.aj - empty
Deleted SRC_MAIN_JAVA\com\example\petclinic\ui\mvc\ApplicationConversionServiceFactoryBean_Roo_ConversionService.aj - empty
Deleted SRC_MAIN_JAVA\com\example\petclinic\ui\mvc\VisitController_Roo_Controller_Finder.aj - empty
Deleted SRC_MAIN_JAVA\com\example\petclinic\ui\mvc\VisitController_Roo_Controller.aj - empty
Deleted SRC_MAIN_JAVA\com\example\petclinic\ui\mvc\PetController_Roo_Controller_Finder.aj - empty
Deleted SRC_MAIN_JAVA\com\example\petclinic\ui\mvc\PetController_Roo_Controller.aj - empty
Deleted SRC_MAIN_JAVA\com\example\petclinic\ui\mvc\OwnerController_Roo_Controller.aj - empty
Is there a way to disable the roo-shell in STS? Without some sort of workaround for this STS is unusable for roo multimodule projects.
So far the only workaround I have found is to use use plain eclipse instead of STS for roo multimodule projects