Hi Mathieu,
Generally, even if those flags are not updated, SAP will not send them twice. Internally it keeps a track of change pointers processed. Though I have not seen them marked as processed. If I am not wrong, there are few SAP notes on that, which I can find later and update the thread.
We generally, don't worry for this flag (because SAP will not send data more than once) and at the same time, schedule the job for deleting obsolete change pointers from tables due to performance issue.
I hope this help.
Regards,
Amit