Hello Harshil,
the certification should not affect the S-User IDs.
The reason is that there are several S-Users who do not have any certifications, yet they can fully use their S-account (or the status of their S-account is being changed independently of any certification results).
Also, the certification is "just" an addition, which should not do anything to the main account.
(For example: I can't imagine an S-User ID will be closed with the reason "Your knowledge is too old". It sounds more comical than serious... 
)
Best regards,
Laszlo