Between doing everything it can to support two rebellions across two continents plus the fact that there are lesser Scions involved still in tracking and watching the Beast Tribes to make sure they aren't summoning primals, combined with the fact than frankly the organisation is far less centralised and you can see why expenses might have started to become an issue. The Scions have tended to be fussy on what revenue streams they accept and its possible they haven't fully been rebuilt since the Scions fall from grace.