If they were successfully linked at one time, then most likely a change was made to the available blocks for each course so they are not the same.

Linked courses must have the exact same blocks selected for each block type on the Schedule tab of each course that is to be linked together. If the blocks match for the Academic block type on each course, but the course to be linked does not appear in the Linked Course dropdown, check the other block types and ensure the same blocks are selected for each course.