Is there a way to adjust trade data between China and EU member countries for the Rotterdam effect?
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.