Gareth, please read my reply to the the post "Merge on web." It has a great deal to do with "Smart Matches" causing problems in your tree. Please beleive me, I am not the only one who has encountered an enormous issues with these so-called "Smart Matches." I would repeat what I wrote here, but it is lengthy and easy enough to read it on that post.
If you Merge a record, only the selected person or people are merged.
Hope this answers your question.