Systems and methods for performing apheresis procedures, including photopheresis, are disclosed. The systems and methods utilize a disposable fluid circuit that can be converted from a double needle configuration to a single needle configuration and from a single needle configuration to a double needle configuration. A controller directs the action of system pumps to clear potentially stagnant blood residing in the fluid circuit, tracks system parameters and status before and after conversion, and verifies that the procedure may proceed in its new configuration.
