I have a sphere merged with a box with retained the boundaries

I am now trying to mesh this merged part. I would like to have a continuous mesh & 2 sets, 1st a set of all the elements in the sphere & a 2nd containing everything else.

My problem comes during the meshing as the mesher doesn't mesh the spherical region, see below for typical cross section

I have tried partitioning but I just cant select the spherical region.

Anyone know how to do this?