Unfortunately I am not an accountant so don't know if I'm qualified to answer your question However .... it all seems a bit unlikely that for 6 years somebody would keep a yacht that on the face of it wasn't used by any employee or director (or is it employee of Director as stated in your question and there is more private expenditure of domestics through the company) privately and also if I am interpreting your question correctly only ever gave rise to one charter leasing transaction.
What does the yachts log book maintained by the skipper say that it has done and where it has been in these 6 years. Uncommercial? I'm not sure that is the first word I would think of ... more apt to say unlikely and is this an old yarn for the HMRC inspector.
Alternatively of course the HMRC might be inclined to consider that the Yacht cost and all the subsequent upkeep should have been charged to Director's/participator's loan account with potential S419 duties, old S160 benefits & of course CT into the bargain. I assume that there is no hint that the yacht was actually purchased/mortgaged by the director and how and where were the crew's wages charged through the company accounts.... in wages I trust with appropriate PAYE etc operated. There may be a lot more to come out in this enquiry and perhaps it's a damage limitation exercise that is needed. Alternatively as you say it's just been bad luck that the company (presumably by a decision of the MD) has maintained this large Albatross instead of divesting itself of a continuing bind on its resources.
regards
bill@wamstaxltd.com
http://www.wamstaxltd.comregards and hope this helps
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