This is the main drawback of the qualifier circus. PhD students waste 2-3 years preparing for this arbitrary and nightmarish rite of passage, time that they could have started their research.
I am glad that that particular department decided to do away with the exam. It is better to define a subset of core courses, and just use the GPA in these courses as a qualifier for formal admission into PhD candidacy. This will help the students gain the candidacy in parallel with the coursework rather than sink enormous amounts of additional time into an exam.