When you remove a model that pertains to an Array of a related model, that array is updated by Ember Data but not stored unless you manually call the parent model save() method.
Currently I'm solving this issue with the following code, but I think this should be automatic?
Board = ParseModel.extend
name: DS.attr 'string'
project: DS.belongsTo 'project', async: true, inverse: 'boards'
didDelete: ->
@get('project').then (proj)-> proj.save()