The batch settlement and clearing of the POS batch requires all registers/terminals to be active (powered on) at that time.
Go ahead and run the end of day and try again. If the batch still does not settle on the POS, ensure the batch is settled on the Pax device (call processor to make sure batch has been received) and then clear it out of the pos system. Again, verify the batch settlement from the processor before clearing batch in the POS.