"Antibodies fit themselves to known germs but if the germ mutates into an unknown structure from having some of it's structure removed the antibody can't connect and destroy the germ."
Well, that's absolutely false from the immunology classes I took long ago at Stanford. While any given T-cell may have a fixed structure it connects to, the antibodies mutate to many forms and eventually one "connects" and that lineage is multiplied. Evolution on the quick at the cellular and molecular level. That's why, despite there being a new swine flue variant every year, we all eventually develop antibodies.
Sorry to not be more specific, it's a bit hazy, but the geneeral mechanism has been known for quite a while. Antibodies are not static.