prad,
the problem you ran into is that editing the BPMN file directly is fine by Designer, as long as it supports everything you're doing - in that case your changes will also be reflected in the diagram view (they have to be kept in sync by the tool for obvious reasons). The BPMN file is a generated file, so it will always be overwritten if you edit the diagram and only with constructs the diagram understands. A bug was fixed where not all of the timer event's attributes were copied and the fix will be in the next release of Designer.
For now, to not lose your changes, you will have to copy the BPMN file and then make changes so they're not overwritten. I know this is a hassle, but at the moment there's no other way to prevent that from happening.
General rule of thumb: yes, if you want to use the full functionality of Designer, you're best off sticking with the constructs it supports or otherwise branching off your BPMN file at a certain point as I mentioned above. To use the full capabilities of the engine, your best bet is to hand edit the BPMN file, which Designer can also help you with by providing schema validation.