On U.S. Navy ships the jackstaff (at the bow) is used to fly the Union Jack, or Navy Jack (Don't Tread on Me) since 9/11. It is not flown while underway, but only when moored, or anchored. When the anchor clears the water, or the last mooring line is dropped the command "shift the colors" is passed over the IMC and the jack comes down. At the same time the National Colors are lowered at the stern staff and raised on the mast. Unless it is a short cruise, or change of mooring/anchorage the jackstaff at the bow is lowered/secured and the staff at the stern is lowered/secured. The only exception to this that comes to mind is during flight ops (helos) moored, or at anchor when the staff at the stern might be a safety issue (LPDs, LSDs, carriers) and then the National Colors would be flown from the mast.
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