In 1689, he sent a memorial to the government, proposing a joint recognition of presbytery and episcopacy. After Killiecrankie he was employed by the government to treat with the Highland clans. He thoroughly understood Highland politics, and his prudent counsel was of considerable advantage in bringing about a settlement. If, says Macaulay, his plan (of distributing a few thousands sterling among the Highland chiefs) had been tried when he recommended it, instead of two years later, 'it would probably have prevented much bloodshed and confusion'. On 5 March 1692, he was restored to the office of clerk register, but resigned it towards the close of 1695. According to Secretary Johnstone, he had been caught 'grossly malversizing in his office of clerk both in public and in private business'.