Alopecia areata results from a disregulation of the immune system against its own hair follicles. When it is very long-standing or advanced, biopsy may demonstrate complete dissolution of the hair follicles. This condition may benefit from hair transplantation, however there is always a chance of flaring the alopecia in unaffected areas where the hair is harvested from. Likewise, it may result in flaring of the recipicent areas as well if there is some hair still present.
To summarize, it is difficult to predict what will happen when we transplant alopecia areata. At the worst, you may lose more hair than you anticipated, and feel you wasted money in the process. At the best, you may get regrowth of hair in the affected areas and think it was totally worthwhile.