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Here's how I solved this:

I seemed to have installations of both kinetic-bfl and lunar-bfl, despite updating my ros version to lunar. So I went back and removed all installations of bfl.

apt-get remove ros-kinetic-bfl ros-lunar-bfl

Then had to clear the cmake cache in my catkin workspace:

catkin_make clean
rm -rf build/

Now running catkin_make in my workspace that had the robot_pose_ekf package, went through just fine.

OS Version: Ubuntu 16.04.3 LTS ROS Version: Lunar

This line needs to read orocos-bfl (as below) and not just bfl (as in the roswiki)

pkg_check_modules(BFL REQUIRED orocos-bfl)