The old canon novel Darth Plageuis established that the Force itself created Anakin as a reaction to Plageuis and Sidious attempting to wrest control of the Force. Now, it's not technically canon anymore, but the new canon novel Tarkin references several events of that novel so I consider it to be canon still.
My guess would be to treat those references the same way the new DC universe treats events before Flashpoint. Writers can reference events that happened in the previous continuity, but the reader shouldn't assume that that means other events happened.