I suspect one is dealing largely with two subjects.
VAT and flagging.
If EU VAT has been paid on he boat then as long as it isn't BREXITED, the boat should retain VAT status.
As to flagging, in the USA it is called documenting. The boat is either flagged by a
member country of the EU or non-EU flagged. If you are an American citizen then you can document the boat with the Star Spangled Banner.
There is no EU flagging of a boat, it is country specific matter and you need to evaluate the rules of being able to flag your boat in a foreign / non-USA country.
Other issues may arise if you have dual citizenship or if you have EU resident status.
If you are a resident of a country that country may avail flagging of your boat, you will need to
research the country specific laws in that regard.
Next issue, as to importation, temporary or otherwise, reference and copied snipet therefrom: I would recommend that you cross verify this matter with additional sources and authorities.
http://www.dohle-yachts.com/wp-conte...on-into-EU.pdf
Temporary Importation to EU
If a yacht operates in EU waters Value Added Tax (VAT) and
customs duties must be considered. These considerations can also impinge
on the choice of Flag State, the yacht’s
ownership structure and the place of
ownership.
The EU’s Sixth Directive on Value Added Tax was amended in 1993. This amendment states that all yachts which are
owned or used by an EU resident in EU waters must pay VAT or have proof of VAT exemption. Failure to comply with
EU
regulations can have serious consequences for a yacht and its owners – this can include detention or seizure of
the yacht, or severe financial penalties.
It is therefore vital that the yacht complies with all
regulations and has appropriate ownership structures in place.
Owners who are non EU residents, or a yacht which is non EU Flagged, who wish to sail their yachts in EU waters for
private purposes may temporarily bring their yacht into the EU without
customs duties or VAT needing to be paid.
The
boats concerned have to be placed under the 'temporary importation procedure' (TI) with Customs and the period
of use in the EU is limited in time to eighteen months. The temporary importation rules are covered under Article 562
of the Customs Code. When the time is up the boat has to leave, in official jargon this period is called 'the period of
discharge'. The re-exportation of the goods from the customs territory of the Community is the usual way of ending or
'discharging' a temporary importation procedure. If the boat does not leave before the end of that time then customs
duty and VAT become due.
A boat is temporarily imported into the EU and not into one of the constituent
Member States. Thus it can move from
one Member State to another with no further customs formalities during the 18 month period allowed.
After 18 months the yacht must be exported before re-entering the EU under the same rules.
How can a yacht be placed under TI? Just crossing the frontier of the customs territory of the Community is in general
sufficient. But, the yacht may be required to use a
route specified by customs and they may require the vessel to
make an oral or written customs declaration. It is possible that customs may require the provision of some kind of
security or guarantee to cover the payment of the customs duties and VAT that become due if the boat does not leave
the EU.
The legal provisions on temporary importation are found in Articles 562 and 137 to144 of the Customs Code.