It became necessary to find a replacement as commander of the squadron, and Admiral Sir Michael Culme-Seymour, 3rd Baronet, was appointed. Culme-Seymour first acquired as secretary Staff Paymaster Henry Rickard, formerly secretary to Admiral of the fleet Prince Alfred, who had just ceased to be commander in chief of Plymouth. Culme-Seymour next telegraphed to Evan-Thomas, requesting that he would take the post of flag-lieutenant. Evan-Thomas hesitated, because the post was at least on paper less than a lieutenant of his seniority might expect. However, the request was endorsed by Admiral Lord Clanwilliam, and also the first sea lord, Sir Anthony Hoskins. Evan-Thomas went to see both admirals who assured him he had been chosen on merit, as it was felt that under the circumstances the best man possible was required for the post. Culme-Seymour was concerned to restore the efficiency of his squadron, in particular through exercises to build the confidence of his ships' captains that they could work together effectively and without further mishaps. Evan-Thomas gained considerable experience in working with a fleet, and in particular a comprehensive knowledge of the signal book. Control of a fleet at this time was by a system of flag signals from the command ship, which had to be read and obeyed by other ships. The signal book had grown to contain thousands of flag combinations to give detailed instructions, and controversy had arisen within the navy whether this system would be practical in battle. Tryon had been an advocate of a much simpler system, where captains had greater latitude simply to 'follow the leader' and use their own initiative rather than waiting for explicit orders. Ironically, the ship collision had happened during manoeuvres using the traditional system, not when captains were supposed to be acting independently, and had they used initiative rather than following incorrect flag commands, the accident could have been avoided. Nonetheless, a perception arose that the simplified system giving more independence to captains was somehow to blame, and the navy as a whole moved back to detailed flag instructions. Evan-Thomas at the centre of this reversal of policy in the Mediterranean squadron, gained an expectation for accurate and detailed flag commands which contributed to later difficulties at the Battle of Jutland, where signal failures contributed to the loss of British ships. Other experiments continued to try to improve the effectiveness of communication between ships, including semaphore, searchlight and carrier pigeon. Evan-Thomas continued to suffer from illness while in the Mediterranean, and in 1894 received sick leave to return to England.