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It has, yes. Apart from many roundabouts and town centre alterations there's bridges cutting corners on the coast in Scotland (there is a new road on Helmsdale which is about 1 mile SHORTER than before) as well as the finish line (The old finish line at JoG is no longer there. The old hotel is now private flats. The new finish point is the leading edge of the mini roundabout about 68 yards BEFORE what was the old front door.). John Taylor's LEJOG book goes through some of the course change details in documenting the attempts over the years.
I believe the LEJOG route has been changed several times over the years.