Here you have more information:
Kroatien: Nachversteuerung zu 5 Prozent kommt! - Reise*|*YACHT.DE
I don't think the problem would be with Croatia. Regarding Croatia if they say you have the VAT paid, you have the VAT paid and that's finish.
The problems is how the other EC countries are going to look at this maneuver that is clearly a way of evading tax in their countries and what they are going to do about it?
Maybe nothing because this is just a transitory 3 months measure. I guess it will depend on the number of sailors that will try to take advantage of this.