The problem is that Europe have a long urban tradition and most European capital makes a lot of sense and even if they didn’t you would simply move the capital to another city which would make sense.
This is true, but after the Zuiderzee in the Netherlands was turned into the IJsselmeer by building the Afsluitdijk, after that the Noord-Oost polder and Fleovland were reclaimed from the sea. In 1986 they became the 12th province of the Netherlands, almost completely consisting of reclaimed land (two former islands in the IJsselmeer, Urk and Schokland, were incorporated in the Noord-Oostpolder). Today Almere is on of the largest cities in the Netherlands, even though it's only established in 1976. Other cities in the province, like its capital Lelystad, Dronten and Emmeloord were established in the 1960s. So with a newly build province, we're already half way there.
I don't immediately see how one of those cities becomes the capital of the country, but the Netherlands already has the somewhat unique situation of having a capital, Amsterdam, which is not the seat of the government, that's The Hague. I don't think a worse WW2 will do it. Even if The Hague or Amsterdam are completely flattened, there's to much history there for not to rebuild it. Maybe a worse storm in 1953 will do it, flooding more parts of Zuid- and Noord-Holland leading to Amsterdam and/or The Hague being abandoned, while Flevoland survives and government takes its seat there. But such a storm might be ASB, and Flevoland not the obvious choice (there wasn't much there yet).
A few years ago there was a miniseries "
Als de dijken breken" which had the premise of a bigger storm than the 1953 one hitting modernday Netherlands, leading to a big part of the country being flooded (and a part of Belgium too). A modernday storm, or in the 90s, might do it.