We export goods to India from Felixstowe, via Rotterdam, where they are transhipped from a feeder to a deep sea vessel. Should the Felixstowe to Rotterdam stage of the shipment be reported under Intrastat?

No. Your intention is to export the goods out of the EU, and you must therefore complete normal indirect export formalities for shipment of the goods from the UK to India.This means completing an Export Accompanying Document (EAD) as the partial export entry in the UK and this must accompany goods to Rotterdam. It will be used there by the Dutch authorities to complete the export entry outside the EC. You should ensure the EAD has been completed within 15 days of opening by using the Europa MRN transit database  http://ec.europa.eu/taxation_customs/dds2/ecs/ecs_home.jsp?Lang=en

NB: Goods being imported into the UK from outside the territory of the EU may legally be cleared at the first EU port of call (often Rotterdam bound for the UK). The onward journey to the UK could be reported under Intrastat; however, it is preferable that the appropriate import documentation is used to cover the whole journey from the extra-EU country (e.g. India) to the UK, including transhipment in the original port of arrival in the EU. In the case where Rotterdam is the port of transhipment, the goods were never intended to be imported into Holland and clearance there, with an onward Intrastat movement to the UK, can skew Dutch trade statistics. 

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