The figure below shows a typical ECO flow. You open a previously implemented design. After modifying the netlist, if the design is not fully placed, you run Incremental Place.
Otherwise you can skip straight to Incremental route. After that you can save your changes to a new checkpoint and write new programming and debug probe files and Open the Hardware manger to program your device. If you are satisfied with your changes you can incorporate them into your original design. Otherwise, you can start at the beginning of the ECO flow until the design is working as expected.