All the studies I've encountered that have monitored the brain and neurons in humans long-term after MDMA use to date have had similar findings- some suggest it takes 3 months for full recovery, others have found up to a year. I am sure severity and duration of use are a huge factor, along with age. The ultimate findings were that MDMA can have devastating effects for some time, but the issues all seem reversible with abstinence.
That said, the human body and brain is extremely complex, and we still only know a small portion of the information there is to learn about it. Scientists are finding out new things about the body every day- and MDA is a relatively new and unstudied drug compared to many. I am sure there are plenty of things yet to be discovered about it's effects short and long-term.
This article does not bring up anything new or conclusive. I would be open to seeing a study that shows proven evidence of long-term damage, but keep in mind studies are flawed. The famous study funded by the FDA in which a scientist used "mislabeled" methamphetamine to study the effects of MDMA drew all sorts of false conclusions that still get quoted to this day- I meet people weekly in clubs/raves who think "ecstasy puts holes in your brain/causes Parkinsons" etc. due to this false study that was done a whole decade ago.