I use Core Data to store large amounts of 3D vector data.  I solved your 
problem in the following way:
 
I have a "Vector3D" entity that you can think of as an "end point" in your 
model.  My Vector3D entity has x,y,z attributes.
 
I have a "Vector3DReference" entity.
 
Vector3D has a "to many" relationship to Vector3DReference which has a "to one" 
relationship to Vector3D.  I can ask any Vector3D for all of its references, 
and I can as a reference for its Vector3D.
 
Vector3DReference is abstract.  I have derived Vector3DReference for all of the 
cases where I have other entities with relationships to Vector3DReference.  For 
example, I have a Billboard entity that has a "to one" relationship to 
BillboardAnchorVector3DReference which has a reciprocal "to one" relationship 
back to Billboard.
 
It is common in 3D systems to have a large collection or database of 
points/vectors and then reference the points/vectors for index or ID.  E.g. 
consider multiple triangles that all share a vertex. When the vertex changes, 
all of the triangles that share the vertex are updated.  Sharing vertex data 
also reduces the storage required vs. lots of copies of the vertex.
 
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