Mr & Mrs Parsons from Cumbria, where the ad was shot, did not want Badger, their 34ft yacht to be associated with McDonald's.
Leo Burnett is not believed to have been in breach of any copyright regulations, but removed the boat as a gesture of goodwill toward the couple.
The re-edited version of the ad, which is currently off air, will re-launch in December.
Launched in June, the original campaign was filmed in Derbyshire, Cumbria and Staffordshire at the farms which supply McDonald's with organic milk, free-range eggs and potatoes.
It tied in with a positive spin on British weather and how it is integral to British farming, shown through large rain cloud and snow flake weather icons.
Media was bought by OMD and planned by Andrew Lloyd.