The following code is from SalFlowServiceImpl.updateFlow (and annotated):

//STEP 1: HERE THE FLOW IS MARKED FOR DELETION BUT NOT ACTUALLY DELETED. THE MARK IS BASED ON THE FLOW HASH

deviceFlowRegistry.markToBeremoved(flowRegistryKey);

if (itemLifecycleListener != null) {
final FlowDescriptor flowDescriptor = deviceContext.getDeviceFlowRegistry().retrieveIdForFlow(flowRegistryKey);
if (flowDescriptor != null)

}
//if provided, store flow id to flow registry
if (flowRef != null) {
final FlowId flowId = flowRef.getValue().firstKeyOf(Flow.class, FlowKey.class).getId();
final FlowDescriptor flowDescriptor = FlowDescriptorFactory.create(updated.getTableId(), flowId);

STEP 2: HERE THE FLOW IS RE-ADDED...
deviceFlowRegistry.store(updatedflowRegistryKey, flowDescriptor);

STEP 3: STEP 3: DeviceFlowRegistryImpl.removeMarked is called resulting in the removing of a flow that should not be removed because it was in fact re-added right afterwards. Next time the flow is updated via an OFPST_FLOW it is missing the flow id and therefor receives a generated "alien" id.