To replace an asset with a new version, you can use RAMSession.replaceAssetNewVersion(Asset, String version). This will return the same object passed in with its version set to the new value. The GUID will remain the same. Once this asset is committed, only this asset will exist on the server.
// Create a new asset to submit to the server
RAMAsset newAsset = session.replaceAssetNewVersion(newAsset, "2.0.0.1");
// Set asset metadata
newAsset.setName("New Asset");
newAsset.setCommunity(session.getCommunity("Rational Asset Manager Development"));
newAsset.setAssetType(session.getAssetType("Documentation"));
newAsset.setShortDescription("Sample upload asset");
session.put(newAsset, new NullProgressMonitor());