A colleague at the University of Edinburgh just found the following while researching something else:
CH2/361/1: Presbytery of Uist
6 Aug 1798, at Valay, North Uist
Compeared Christian MacEachin of the Roman Catholick persuasion, from the Island of Benbecula, fathering a Child born by her in fornication April 27th 1797 on John Butter Esq late Factor for Clanranald and complaining of Mr George Munro Minister in South Uist for having rashly taken the Oath of Mr Butter signifying that the Child was not his, while at the same time he acknowledged guilt with her, the Presbytery after having seriously weighted the nature of this delation & complaint find that as Parties are not before them, they are not competent to pronounce judgement in the cause, but that as it appears Mr Butter is about to leave the Country, and the Child unprovided in mantainance [sic], They enjoin Mr George Munro to cite the Parties before the Kirk Session of South / Uist, and to proceed in the cause according to the regulations of the Church, with a view to prove the Father of the Child, not sustaining the oath of any man assoilvied who acknowledges guilt with the woman. The woman being called in, an extract of this minute was given her signed by the Clerk.
The reference to John Butter leaving the country fits with John Scott Butter's move to the East India Company. I still of course need to reconcile the report of his death in 1800 with the Clanranald papers which suggest he was alive after that.