Is there a way to adjust trade data between China and EU member countries for the Rotterdam effect? Basically Eurostat trade data for individual EU member countries with China seems to have some substantial artefacts probably because most EU imports from China arrive in Dutch ports, even though their ultimate destination is probably all over the EU. It's hard to explain otherwise the huge figure for Dutch imports (and thus trade balance) from/with China relative to Dutch population, economy, etc.

Are there any data sources or papers that try to adjust for this Rotterdam effect, i.e. figure out where those Chinese imports are really headed in the EU (and adjust the trade figures per member country accordingly)?
(Thanks to Henry for pointing out the right term.) Eurostat actually acknowledges the issue in a FAQ, but does not try to quantify it:

The quasi-transit is known to impact mostly the Member States with big ports at the external border to the European Union and in particular the Netherlands. This is why its impact on figures is known as the ‘Rotterdam effect’. In case of imports, the goods destined to other EU Member States arriving in Dutch ports are recorded, according to Community rules, as extra-EU imports by the Netherlands (the country where goods are released for free circulation) and as dispatches from the Netherlands to the Member States of actual destination even though there is no link with economy of the Netherlands.
The quasi-transit is known to impact more the imports but exports are also affected. In exceptional cases, the customs clearance occurs not in the actual Member State of export but in the Member State of exit, i.e. in the Member State from which the goods are taken out of the EU customs territory.
This seems relevant: China and the Dutch Economy

I have only a limited experience in this, but here are some approaches you could look at.

Re-export data

UN Comtrade has re-exports data (products that the Netherlands import and export in the same form to other countries). Using this, you could make an assumption that x% of goods imported from China are re-exported to the EU. Assuming that this share of re-export actual source countries are the same for Dutch exports to the EU, you could get a rough estimate of how much goods from China goes to each EU country. 

Using aggregate data, this could be a very far-off estimate. Belgium could import a lot from Netherlands, but all it imports are tulip flowers. To account for this, you can look at this on a HS-code level and you should get a reasonable estimate.

TiVA

Another approach is to look at the TiVA (trade in value-added) concept. This should tell you each country's value-added into an import of a country. OECD has this data, but I don't believe it covers all EU-28. Here's a link.