Firstly since VAT is not ( in all normal cases) paid directly to the fiscal authorities ( unless the boat was personally imported) mosty people simply have effectively a "letter" ie an invoice saying you or someone( possibly) paid VAT. Its not possible to get confirmation that say VAT was paid by a dealer on your behalf, as VAT is not collected on a specific item, its paid as a balance between purchase
VAT and Sales VAT.
This actually why instances of VAT inspection
are so rare. VAT is the preserve of the country in which you bought it. You cannot be asked to pay French VAT on a say UK boat. ( unless the french authorities are convinced you are personally importing it). Invoices are just pieces of paper that have no real relevance.
The key thing you need to show is that the boat was in a EU country when you bought it. Then VAT is the perserve of that country. Registration
is one way.
Theres a huge nonsense about on the internet
about boat VAT. Until I hear a story directly first hand where someone has had their boat seized until they paid teh VAT, I;ll not beleive the nonsense I hear.