Not exactly sure what controller you are talking about, but with in reason just about any brushless hub motor can have the voltage increased. I like to experiment a bit with different voltages through the common controllers that come with most kits. I have found them pretty tolerant of voltage increases. They are so cheap doesn't matter much if I blow one. I am currently running 48v thru my 24v 250w system without issues to this point. It just requires the ability to monitor the voltage and cut operation when the batteries low voltage is reached. This voltage increase raises the 250w motor to 816w and turns a rather sedate bike into a bit of fun.
Ideally just buy a controller at what ever voltage increase is reasonable, match the battery to it and go. However try not to over amp the system unreasonably.