If needed you can manual archive your Transport Order just by filtering and selecting the Transport orders which are completed/done
In the transport order list page there is a field Archive Transportorders. The orders will be archived directly and if needed available in the archived transport orders.
In the taskscheduler you can find jobs which can be helpful to update statuses of you Transport Orders and for periodically clean up the Transport Order table.
Codeunit 11147661 IDYS Scheduled Tasks Handler can be set with the following strings:
TransportOrders do have a separate no. range. Setup a preferred No.Series for the creation of the Transport Orders.
Need more help with this?