Unfortunately, you can’t use modeling.udpateProperties for nested properties like the ID of a referenced process. If you want to change the ID in a way that allows undoing and redoing you have to introduce a new command handler. The bpmn-js properties panel has a handler for this purpose: https://github.com/bpmn-io/bpmn-js-properties-panel/blob/master/lib/cmd/UpdateBusinessObjectHandler.js
You can use this handler or create your own.