Hi Davorin,
Did the corrected process only contain a fix for the default flow issue, or were there more changes?
If there are no other changes the best solution would be to point running process instances to the new corrected process definition using the org.activiti.engine.impl.cmd.SetProcessDefinitionVersionCmd class.
Using the org.activiti.engine.ManagementService executeCommand method it's possible to execute this command and change the process instances one by one to the new process definition.
The property you are referring to for enabling/disabling safe BPMN parsing is not relevant.
Best regards,
Tijs