I think the american registry of pathology who actually runs the course will continue to exist. Also, during the course, they don't really use a lot of specimens or other things that really need the institute for. Most of the lectures are slide/powerpoint based and the faculty comes mostly from institutions outside of the AFIP (most are AFIP almuni though).
The problem will be that right now there is that critical mass of pathologists and radiologists in one place. Most of the AFIP lecturers were also USUHS faculty, I would hope that they continue the course maybe somewhere out at the planned campus in Bethesda.