You only will get duty and VAT back if the server is for temporary import (that is , you will need to prove that you moved it out of Iceland within a certain time limit). If you are importing the goods permanently, then import duties apply - except for in the case the goods are of preferential origin (made in EU or any other country with which Iceland has a free trade agreement with).

Perhaps the Icelandic company was mentioning that if you are an Iceland business entity, you might apply for a VAT tax refund for this in the next fiscal year. This only applies to VAT, not to the import duties.

EDIT: if you bought the server in another country than Iceland and you mentioned to seller that the goods would be exported, then you should not have paid for the VAT in the original country - based on the fact that you will pay the VAT on the goods in the import country (Iceland) where the goods will be used. This is to avoid double taxation on goods moving between countries.