I think you are going to have to pay the VAT again. The paragraph you referred to has 3 conditions which you probably don't meet.
A boat previously VAT paid and exported from the EU may also qualify for relief on return if:
imported normally within 3 years of its export from the EU
imported by the person who exported it from the EU
it has undergone no more than running repairs outside the EU that did not increase its value
Your options are do nothing particularly if you have a copy of the original VAT receipt, or write to HMRC for
advice because you will want the answer in writing, but you will tip HMRC off about the transaction if you do. Suspect the VAT is going to be a large sum on a 16m 2.5 yr old yacht.
There might be one "get out" that is importing something called "chattels" which allow you to return to the UK with your possessions without paying duty on them. You will need advice from HMRC if the yacht will qualify.
Pete
Pete