Right. I’m stumped. As ever several other people.
As detailed in this support forum post I have my main index file (this page) outside the directory WordPress is located. WordPress presumably allows this as you specify a different directory for the WordPress URI to the Blog address URI. However, when I edit my template, it edits the one that exists in the WordPress URI rather than the one that exists in the Blog address URI (this is explained better in the forum post).
So, anytime I change my WordPress template I need to manually move it from the WordPress install directory, to the root of my site (the Blog address). What’s the point in that? I say it’s a bug. Any other WordPress users wanna contradict me? Set me straight? Offer a solution!
UPDATE: I’ve logged a bug.