He was in the Mercury bound for America in 1784 when she was seized by the convicts off Torbay; he was recaptured and held at Plymouth until transferred to the First Fleet transport Friendship.
David Collins stated:John Baughan, an ingenious man, formerly a convict, had undertaken to build another mill upon a construction somewhat different from that of Wilkinson's, in which he was assisted by some artificers of the regiment.
[3]On 24 December 1793, the millwright and Baughan had got up the frame and roof of his mill-houses and, while waiting for there being tiled, was proceeding with preparing the wood-work of his mill.
[3] The grinding mill commenced operations on the 10 March 1794; with nine men working its capstan bar, it ran so smoothly that sixty-three pounds (29 kg) of wheat were ground in seventeen minutes.
James Wilkinson's mill nearby, powered by six men who walked inside a massive wheel, commenced operations a month later; it was soon abandoned and Baughan was commissioned to replace it by another of his own design.
On 4 February 1796, overhearing himself being abused by a sentinel who apparently bore him an ancient grudge, Baughan slipped out of his workshop, collected his traducer's arms from his deserted post and handed them to the guard.
Baughan, after some days had elapsed, swearing positively to the persons of four of the principals in this transaction, a warrant was made out to apprehend them; but before it could be executed, the soldiers expressing themselves convinced of the great impropriety of their conduct, and offering to indemnify the sufferer for the damage they had done him, who also personally petitioned the Governor John Hunter in their behalf, the warrant was withdrawn.