Are you using eclipse editor or web-designer?
The problems seems to be related to the issue that no default type is set when you add a gateway.
From the issue you have mentioned:
"So the work around is search for all the complexGateway and change them to either exclusive or parallel Gateway, and now you can save and update and change the flow instead of lowercasing it in between. There shouldn't be complexGateway in BPMN2 anyway."
Can you isolate the problem to a simple process and post it here?