Hi @Saad,
what you say is not completely true.
Whithout the option enabled
Briefcase downloads a list of submission instanceIDs and starts to check if the instance IDs where downloaded or not and in case yes it skips it.
If you have millions of submissions imagine the time lost on checking this.
With the option enabled it bypasses this check and goes directly to pull the new submissions.
Without the option enabled:
With the option enabled:
more detailed info on this forum post and here