Will it affect you?

UK-based vessels will lose EU VAT-paid status on ‘no-deal’  Brexit-day or at the end of any transition period. However, if located, at that time, in an EU port or sailing in EU waters it will keep its VAT-paid 'Union' status.

It should be borne in mind that non-EU citizens sailing in EU waters will only be allowed to stay, in person, for a maximum of 90 days in any 180 whilst then leaving their boat in the EU in order to retain its Union status.

A UK-based yacht will lose it’s EU VAT-paid status and become liable again 18 months after any sustained period of re-entry into the EU (i.e. on expiry of EU ‘Temporary Importation Relief’).

In summary, UK-based yachts wishing to stay in the EU longterm should be located in an EU port on Brexit day in order to retain their EU VAT-paid status (keeping marina receipts, dated photographs, insurance certificates etc as evidence).  Conversely, a British ‘EU-based’ yacht may become UK-VAT liable when eventually 'imported' back into the UK (currently after 3 years).

https://www.theca.org.uk/news/rats/considerations_if_no_deal_brexit_070119

see News item ‘T2L’ 13th Dec 2018 for instructions on completing the application form.