vmx file had four extra entries at the end, three of which were empty parameters. vmxd had a different VM id for the clone - which seems sensible - otherwise it was the same (though in a slighlty different order.) I did not try setting the orginal to match the clone. Emptying the original to match the clone did not fix the shrink issue. vmsd file of the original contained some entries although I had deleted all snapshots, The clone version was empty. I did a comparison of the VM configuration files in the original and the clone: But I was allowed to shrink that successfully so I simply deleted the original (well, actually I moved it off to a backup disk just in case anything went wrong.) I made a full clone of it - which was just as big. I have managed to do this, or at least work around the problem.
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