This is how they answered my question.
Hello,
Thank you for contacting the Blade and Soul Support Team.
As for your inquiry, please note that this is the intended design for those specific quests as it allows new and returning players to benefit from playing the new Story. People who already played those story missions will not be able to get the points but it doesn't prevent those players from reaching Stage 2 and ultimately completing Soul Boost Season 2.
You may check what Green Storm stated in the forum: https://forums.bladeandsoul.com/topic/253778-soul-boost-bug/?tab=comments#comment-2104937
If you think improvements could be made to the mechanics behind this, we encourage you to post your comments on the forums, where our Community Team gathers player feedback so they can suggest game improvements to our development team: https://forums.bladeandsoul.com/en/
Please let us know if you have any other questions.
Regards,
GM Pyriel
NCSOFT Support Team