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I should link to the press release too: https://schoolsforchiapas.org/part-four-and-first-approach/
It doesn't sound quite as dire as the article makes it seem. This was deliberated on and planned years ago, and it's above all else clear that this isn't the end of their movement as a whole.
They are doing a big reorg. Likely retooling for defensive action from the sounds of it.
The end of an era 
the group cited waves of gang violence that have hit the area of Chiapas that borders Guatemala
okay so the usual culprits are the source of this
I hope this is just a part of streamlining the MAREZs into the new CRAREZ system
So I talked with a Mexican friend who knows stuff. He says that they are winding down because they cant attract new members. The risks from increased police, military, and cartel presence and the increased benefits from the Mexican government under Amlo have shifted the cost/benefit against the Zapatistas. There were also internal issues over leadership and accusations of nepotism.
He says this isn't a "retool" or "tactical retreat" it is a surrender.