Scalan did not escape entirely the attentions of the authorities and was completely destroyed after Bonnie Prince Charlie’s failed 1745 Jacobite Uprising. Catholics were presumed to be Jacobites. As Bishop John Geddes wrote: “The Scotch Catholicks were generally desirious of the restoration of the family of Stewart to the throne of Britain; nor is this to be wondered at… the Scotch Catholicks were discouraged and much exposed to oppression; it was therefore natural for them to wish for an event, that was likely to relieve them and put them again in possession of the privileges of free born citizens.
By this time, almost 200 years after the first Penal Law were passed, the Government was no longer interested in how we worshipped God but they were mightily concerned about our politics, and when Bishop George Hay instructed Catholics in 1780 to start praying for the King in London rather than the “King over the water” it was a significant step in helping Catholics to emerge from the catacombs and to begin to play a fuller part in Scottish society. In 1793, The Catholic Relief Act was passed repealing many of the Penal Laws. The remote location of Scalan was no longer necessary, so a new college was established at Aquhorties, near Inverurie in 1799 and, in1829, the year of the Catholic Emancipation Act, a further move was made to Blairs, near Aberdeen. Blairs itself closed in 1986 when a specialised institute for young people of secondary school age was no longer thought necessary.