Yes, you can manifest your Royal Mail OBA account more than once in a day. As long as you have done so before your cut off time, all shipments booked between the first manifest time and the next, will be on the next manifest.
If you encounter any issues, please feel free to contact our support team. You can call us on 0117 403 4313 (UK) / +1 (629) 666-6726 (US) or reach us online here.