Dear Karthick-SK1,
Just for not serving the complete notice issue of the service certificate with the negative remarks is unheard of. Possibly there could be more than meets the eye.
Anyway, at this stage, I recommend you submit the application for the fresh issue of the service certificate without any remarks. Address it to the MD of the company. In the application, you may write what were the constraints in working at the new location and your willingness to make a payment in lieu of the unserved notice period. Let us see what he says. If required, you may ask for his interview and beseech him. Let us see what does he say.
By the way, what is your designation and how many subordinates did you have?
Thanks,
Dinesh Divekar