I guess it depends on how important the certificate is to you, your student, and your style/organization.
If it were me, I would be fine with promoting the student and ordering the certificate to be given at a later date. It's just a piece of paper, just like the belt is just is bit of cloth. The student can continue to train at the next level under you, the paper should not change that.
I've never graduated/promoted a student in martial arts, but in my "day job" I supervise the training of resident physicians. If we don't have a certificate ready, we give them a "place holder" in the graduation ceremony and send them the officially signed certificate later. Actually, most of the time, we use place holders since the certificate is a very legal document which signifies the completion of their training. Since graduation ceremonies typically take place a week or two before they are done with their clinical duties, we often withhold the real thing until they have completely discharged their duties.