Both brothers were again returned for East Looe as Court Tories in 1690, and continued to sit for the borough until 1698. In early 1692 Charles Trelawny resigned the colonelcy of The Queen Consort's Regiment of Foot (the former 2nd Tangier Regiment) in protest over King William's supposed partiality to foreign officers, and Henry replaced him as colonel. He left with the regiment to campaign in Flanders in March, and as a result came to be regarded as a court supporter in Parliament. Trelawny was again absent from Parliament in 1693 with his regiment in Flanders, where they fought at the Battle of Landen. In November 1693 Trelawny was appointed Vice-Admiral of South Cornwall in place of his elder brother, Bishop Trelawny. In this post, he was active in raising men for naval service over the next few years. While generally a court supporter, he was thought likely to oppose the proposed Council of Trade in the 1696 session. He signed the Association Oath and, unlike his brother, supported fixing the guinea at 22shillings. In 1696 he was a commissioner for receiving subscriptions to the abortive land bank project.