A commenter suggests:"Why not, as with deceased people, pass a data file over to IRS and let them tell us any ID that got a FSA payment that is over the AGI limit. That way FSA does not have the data but IRS can tell us potential issues with ID's that have earned too much money to be AGI eligible. This should become easier as we move to direct attribution."
Seems to be a good question, but there's a catch. (Rule number X, there's always a catch.) Once you die, your Social security number is no longer private (just ask the genealogists who look at the Social Security death index). So SSA has no problem telling FSA who is dead. By contrast, periodically IRS gets beaten about the head and body about its abuses of taxpayers and releases of their information. (I believe Senator Grassley may even have been on the Senate committee that did the last set of hearings in 1998 or so.) Indeed, before I left USDA the Republicans (probably) passed a law putting big obstacles in sharing data among agencies. That act has probably been modified since 9/11.
So, IRS is very very reluctant to bend the laws restricting access to individual earnings data. I haven't located the description of their system of records required under the Privacy Act, but presumably they'd have to modify it to authorize this processing. That's assuming President-elect Obama calls in an attorney and says it's got to be done. (Of course, then you'd have all the Republicans calling him down for doing something the Democrats complained about when Bush/Cheney did the same thing.)