I am using a @SharedPref, that I am referencing as a @PREF in other classes. It gets generated correctly on incremental builds, i.e. when I save the enclosing file. But on project->clean it is missing.
I have debugged a bit and found (I hope) the most likely culprit for my problem. When the annotations are processed, in the "clean-case", the @SharedPrefs class doesn't exist yet. This case is guarded against by this statement:
com.googlecode.androidannotations.helper.ValidatorHelper.isSharedPreference(Element, AnnotationElements, IsValid):Line 637

        if (type instanceof ErrorType) {

However this doesn't seem to work correctly (at least not in my eclipse version). Adding

        if (type instanceof ErrorType || type.getKind() == TypeKind.ERROR) {

and the same in com.googlecode.androidannotations.processing.PrefProcessor.process(Element, JCodeModel, EBeanHolder)
however did work. I would think that checking the Kind that is explicitly returned would be better than checking a class, but I don't know the details here very well.
Will you investigate this further on your own or do you want me to create a pull request?