PubMed,
http://www.ncbi.nlm.nih.gov/pubmed, the National Institute of Health's (NIH) online database has a bunch of new abstracts for articles regarding Aplastic Anemia published in November and December. Two in particular showed that having a PNH clone in addition to AA made you more likely to respond to Immunology-Suppressive Therapy (ATG & Cyclosporine) than if you don't have PNH. Here are the links.:
http://www.ncbi.nlm.nih.gov/pubmed/24261566
"The response rate at 6 months was higher in PNH+ patients than that in PNH- patients, both after first- and second-line IST: 68% vs. 45%, P = 0·0164 and 53% vs. 13%, P = 0·0502 respectively. Moreover, 42% of PNH+ patients achieved complete remission compared with only 16% of PNH- patients (P = 0·0029)."
http://www.ncbi.nlm.nih.gov/pubmed/24236830
"Among 22 children receiving immunosuppressive therapy (IST) for AA, 73% (16/22) were PNHpos, of whom 94% achieved at least a partial response (PR) to IST; 11/16 (69%) achieved complete response (CR). Only 2/6 (33%) PNHneg patients achieved PR."
I don't think the articles get into the why yet, just that they were determining a positive correlation. You can't read the entire article without a subscription but sometimes if I find a particularly interesting article and it's in a journal that my doctors get (e.g. the American Journal of Hematology) they can tell me the outcome of the entire article.