In 2005, Ingleby and Hobson Architects was appointed by the owner of The Old Mill, Andrew Nicholls, to carry out refurbishment works at the historic building - part of which involved the removal and replacement of a brick panel wall.
Similar charges against Nicholls were also thrown out.
Hobson told the AJ that the court case was 'a complete fiasco', and described the council's conduct as 'shambolic'.
'We had lots of permission to do things and [the work] has to be seen in context of the whole building,' he added.
Delivering his ruling, Judge Daniel Curtis said that both Hobson and Nicholls had spent 'a great deal of time and professional effort, not to mention money, in undertaking a sympathetic restoration of the building.'
Hobson said that he had been awarded 'several thousand pounds' in costs and hinted that he may pursue the council for further damages.
'This is, possibly, not the end,' he said.