Basically, I cannot select multiple rsids and edit SAINT classifications for xyz variable unless the classifications for xyz variable are the same for all the selected rsids. This makes it really hard to change classifications across rsids, especially since there's no easy way to tell which rsids don't line up.
So far I have found that the easiest way to figure this out is to use the Report Suites API to get a list of classifications for all rsids so I can see them all one screen and single out the offender(s). IMO this is a step I shouldn't have to take!
I think a really easy to fix this is to add a "Use xyz rsid as a template" option, exactly how it's done for custom menus.