Norfolk-based sporting gun specialists Holt's had been instructed to sell a 14 x 7ft (2.96 x 2.13m) Union flag that had been in the family of Lieutenant Nicholas Cory, a senior officer on the Royal Yacht George, since the 1830s.
His descendent Arthur Cory had chosen to sell it to pay for repairs to the family home, Penllyn Castle near Cowbridge in Wales.
However, it appears that Cory family lore saying the flag had been flown by the Leviathan under the watch of Capt Sir William Bayntun in 1805 had become muddled.
The auction house issued a statement saying that the Leviathan flag has remained with the Bayntun family since 1805. Charles Miller, of the specialist maritime and scientific auction house, has been approached by descendants of Captain Bayntun's family who still have his Union flag from Trafalgar along with several other artefacts.
Although they currently have no plans to sell, Bayntun's descendants have come forward to protect the integrity of their relic - one of only three Trafalgar Union flags thought to survive.
It seems the Cory history was correct insofar as a large Union flag was given to their descendant following a yacht race between a schooner chartered by Lord Adolphus FitzClarence, illegitimate son of William IV, and the famous Waterwitch.
However, it is more likely it was the flag from the Royal Yacht (itself a second-class ship of the line) or the racing yacht used in victory over the Waterwitch.
Supported by a painting the Cory family have of the George, that makes it a rare and desirable object but something worth perhaps £3000-5000 rather than the £30,000-50,000 Holt's had predicted for a flag flown at the most famous naval battle in British history.
Accurately dating flags of this period based simply on the weave of the fabric and their dimensions is notoriously difficult as most were handmade by cottage industry. "It demonstrates that family history cannot be relied upon when establishing a provenance. It must be tested as much as possible," said Miller.
Only two other Trafalgar Union flags with cast-iron provenance are thought to survive. That which flew above HMS Minotaur is held by the National Maritime Museum at Greenwich, while another from HMS Spartiate was sold on behalf of the Australian descendants of Lieutenant James Clephan by Miller for £325,000 in 2009 to a US collector.