Apologies for the delay in responding to your posting of February 9.
The word "country" is used here in the sense of "district" or "region", rather than Scotland the country. This usage crops up regularly in writings around that time.
John Butter's movements post-1798 can be outlined from reference to correspondence of his successor Robert Brown. In early 1799 Butter was on Benbecula; around 1800 or 1801 he became factor of the Faskally estate; in 1802 he was from time to time in Edinburgh, and in May 1803 he was - presumably briefly - back on Benbecula.
Incidentally, Henry Butter had another son, Archibald, who was an Army Major and apparently older than John Butter, Clanranald's factor. This Archibald did not long survive his father.