I have been doing some digging and it seems that there is a possibility that Ember-Data Beta-3 will fix this issue. I tried a work around involving the use of a .then after each save followed by a transitionTo to refresh the route (while using Rest Adapter) and after inspecting the response in the chrome console-network it’s evident that the relationship between the parent model and the hasMany is broken by .save() since every other relationship and property are returned without any issue.
This behavior is listed as a bug on the Ember-Data Git Hub, hopefully it is fixed soon.
https://github.com/emberjs/data/issues/1228 https://github.com/emberjs/data/issues/1177
Similar Problem From another User: Ember Data 1.0 Beta - Relations lost because record is not de-serialized after save? - #3 by mcmanus