Even though some of the problems with _XREF_XREF where fixed partly with AutoCAD 2008 SP1 and AutoCAD 2009 you will need this tool to fix existing drawings that has performance problems because of the scale list problem.
This free tool can also be used to apply scales from a template on a bunch of drawings.
Download: Scale List Cleanup Utility
See also Between the Lines
Previous blog posts about annotation scales:
Annotation scaling and annotation scale list in AutoCAD 2008
AutoCAD 2008 and Annotation Scale template
Slow AutoCAD startup or performance