Given their location, I think it would be quicker and easier to rip and replace as TheresaA described than to applique over them. The results will look better, too.
For the blocks that aren't assembled, definitely remove the pink and replace it.
If you do decide to use applique or fusible, I would distribute those blocks throughout the quilt so that they form a sub-pattern. Since half the blocks are done, alternating appliqued and "proper" blocks will make the fix part of the pattern. I would still strongly recommend replacing rather than applique, though.