It seems roo cannot find the backing entity in a controller unless it's imported directly. When my IDE (in this case IntelliJ) organizes my imports, and condenses some imports using the * wildcard, some of my controllers aj files are deleted by Roo.

This is most basic case to reproduce it:

// Spring Roo 1.2.4.RELEASE [rev 75337cf] log opened at 2013-10-13 13:53:20
project --topLevelPackage com.springsource.roo.pizzashop
jpa setup --provider HIBERNATE --database HYPERSONIC_IN_MEMORY
entity jpa --class ~.domain.Topping --testAutomatically
field string --fieldName name --notNull --sizeMin 2
web mvc setup
web mvc all --package ~.web
quit
// Spring Roo 1.2.4.RELEASE [rev 75337cf] log closed at 2013-10-13 13:58:54

Then go into ToppingController.java and replace:
import com.springsource.roo.pizzashop.domain.Topping;

with:
import com.springsource.roo.pizzashop.domain.*;

Then you will get:
Deleted SRC_MAIN_JAVA\com\springsource\roo\pizzashop\web\ToppingController_Roo_Controller.aj - empty