... like running marathons, just know that at some point during all that exertion, your brain will start to eat itself — and it’s not necessarily a bad thing.
The article doesn't explain how it's not a bad thing.
In other words, their brains did a little temporary damage to themselves to protect their overall health in the long run.
It says that the brain's fatty tissues seem to return to normal eventually. It feels like saying that an overuse injury isn't a bad thing because you can recover.