On 1st May, 1660, the newly assembled Houses of Parliament passed a joint vote for the restoration of the ancient government, and a few days later, before Charles was publicly proclaimed, the Commissioners of the Admiralty and Navy, at the instance of the Council of State, issued the following order to their subordinate Board:
In pursuance of an order of the Councell of State of the 5th of this instant May It is ordered that it be referred to the Com^{ rs} for the Navy forthwith to take care that such Standards, fflags and Jacke Colours for the ffleete be forthwith prepared as were in use before 1648 and that they be sent downe with all speed to Generall Mountagu as alsoe that Carvers and Painters be appointed to goe down for the altering of the Carved workes according to such directions as they shall receive from Com^r Pett, who is ordered by ye Councell forthw^{ th} to goe to ye Generall. And the said Com^{ rs} are to give order for the sending downe to the Generall One silke Standard and one silke Ensigne and Jacke and such other silke fflags as may compleate a suite for the Naseby[187].
Instructions to this effect must have reached the fleet before it left England, but the flag-makers had evidently not had sufficient time to prepare the new royal standard, for on the 13th May, on the way over, (so Pepys, then secretary to Mountagu, tells us[188])
the tailors and painters were at work cutting out some pieces of yellow cloth into the fashion of a crown and C.R. and put it upon a fine sheet and that into the flag instead of the State's arms[189] which after dinner was finished and set up.... In the afternoon a Council of War only to acquaint them that the Harp must be taken out of all their flags, it being very offensive to the King.
The Union flag, like the Government, now reverted to its original form, but the right to fly it remained the special prerogative of the State's ships, a prerogative much sought after by merchant ships, and often assumed by them without warrant. For the next half century a long-drawn struggle was waged by the merchant shipping for the possession of this right. It begins with a special instruction sent by the Lord High Admiral, James Duke of York, to the Corporation of Trinity House on 9th March, 1661: