Do you have any evidence or acknowledgment of receipt of Original Certificates? The employee should always record such transactions (audio/Visual) and employees should be a witness to each other. If you have any acknowledgment you may demand in writing under acknowledgment to return your original certificates to be returned to you in excellent condition and these should not be soiled, spoiled, mutilated.
You can try by approaching the good offices of your appointing authority, HOD, Chairman etc. You may try by applying your resources and exercise their influence.
If you can establish that certificates are in the possession of employer you can issue legal notice.
The employer can not keep original certificates without issuing reason and acknowledgment and not at all forever. Employer may at the most ask to show the originals to compare and employee can ask to mark OSV on the copies taken by employer.
If you have served the notice you may tender final resignation and demand your due payments, documents and certificates.
If the good offices do not grant relief you may approach a competent and experienced service lawyer and issue a legal notice.