When an unregistered annotation is read from a SUIF input file, it is automatically registered as a flat annotation. This is done so that the manager knows to write the annotation back in the output.
Annotations are often added to a SUIF file in one pass to record some sort of information, perhaps the results of a data flow analysis. Those annotations may then used in later passes to guide various transformations. Even if intervening passes do not recognize the annotations, they will still be propagated to the output. (It is up to the user, of course, to make sure that the intervening passes do not invalidate the information in the annotations without updating them.)