Just for not serving the complete notice, the issue of the service certificate with 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 about 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 an interview with him and beseech him. Let us see what he says.
By the way, what is your designation, and how many subordinates did you have?
Thanks,
Dinesh Divekar