// Step 1 : get all the CDOObjects you want to download
// Match each CDO root with a local resource in which you want to copy it

// Step 2 : copy all the roots
EcoreUtil.Copier copier = new Copier(true, false);
copier.copyAll(allRootsToCopy);
copier.copyReferences();

// Step 3 : 
for (Resource localResource : createdLocalResources) {
            for (CDOObject remoteRoot : localResourceToRemoteRootToCopy.get(remoteRoot )) {
                EObject localCopy = copier.get(remoteRoot);
                cdoResource.getContents().add(localCopy);
            }
}