When you have populated the FMS [Flight Management System] from your flight planner, always save the flight plan from within your FMS. The saved flight plan is saved as new file in …X-Plane 12\Output\FMS plans folder called XXXXYYYY.fms where XXXX is usually the departure ICAO code and the YYYY the arrival ICAO code.
Question: Why should this be necessary?
Answer: If we ever want to quit the flight and then resume it, saving the flight situation will NOT save the FMS information when flying a default X-Plane aircraft. (Third-party aircraft may be different and often have special systems to do this, however.)
So, if we have this file and then load the saved flight, it is easy to restore the Flight Plan into the FMS. From there, we can load the flight plan back into the ATC window by importing it from the FMS by clicking the button: 