When configuring readers for synchronizing, a slave reader will stop scanning if there is no master to trigger it. The simplest solution to get it scanning again is to connect a master.
Without a master triggering a slave the reader settings cannot be changed due to a bug in the control module firmware from Texas Instruments. The solution to getting control back is to disassemble the unit, flip the DIP switch on the control module. The reader will then respond to commands so slave mode can be disabled. It is important to place the DIP switch back afterward on for proper operation.
See instructions for accessing DIP switch here: