How can we move repository files to another disk on the server?
Will moving repository file directories to another disk on the server cause any problems with reports that have already been rescheduled?
I am not 100% sure if I understand what you mean by a 3-machine config. But no, moving the FRS to a network share does not really alter your system config but only add another component to it. The file store would just be remote on a SAN, but that would not mean you changed you architecture to add another server. I am not sure why it concerns you anyway...licenses or something that bothers you about the multi-server architecture?
In fact, if you do intend to add more hardware to the mix and say, cluster another CMS instance for load balancing/failover along with a redundant set of BO services, the second set of I/O FRS services can easily point (and will have to) to the same shared network location for the files. Instead, if you were to keep the FRS location local to your BO Server as it is today, you would have a hard time "sharing" the file store in a clustered environment.