You have an emf model with many elements, and you want to store them in separate files. Though it is expected intuitively, it gets unduly tricky because of lack of documentation. Here is the essentials
1/3. Make sure you create all resources from the SAME ResourceSet.
2/3. Make sure you create all resources from the SAME EditingDomain (This is actually same as point 1 in some sense, since an EditingDomain has one resourceset)
3/3. ABOVE ALL - MAKE SURE YOU DO THIS LITTLE HACK/ADJUSTMENT/ in the generated .genmodel file.
- Select the root element of the Genmodel.
- Look below in the properties view, for the top level node called 'Model'
- Find the property "Containment Proxies" and set it to "true"
4/4. Of course make sure you save your contained element to a new resource before saving your container. (Else you might have duplicate entries i guess...)
Voila..!!