It had long been identified as a key stategic rail route by the European Commission and a significant amount of EU funding went into the scheme. This funding could have been greater but for a cancellation of the full doubling of track between Soham and Ely. The EU is not a soft touch. If a country doesn’t do the agreed work they obviously don’t get the agreed money.
But it’s nothing new. The UK has a long history of winning EU funding but then not getting all of it because the governmenr reduced, or changed, the project after starting.