I rewrite ModifiersTree:

            TreeMaker make = wc.getTreeMaker();
            List<AnnotationTree> ann = new ArrayList<AnnotationTree>();
            ann.add(ann1.get(1));
            ann.add(ann1.get(0));
            ModifiersTree t = make.Modifiers(fla2, ann);
            System.out.println("ann: " + ann);
            rewrite(node, t);

ann1 is the original list of annotations. The source:

@A1
@A2
class ListOfAnnotations {

    @A1 @A2
    static void m() { }
}


The output in the log is:

ann: [@A2(), @A1()]
original: @A1()
@A2()

modified: @A2()
@A1()

ann: [@A2(), @A1()]
original: @A1()
@A2()
static 
modified: @A2()
@A1()
static 

This is correct. However, the result is incorrect:

@A2
class ListOfAnnotations {

 @A2
    static void m() { }
}