Summary says it all. The style is not superseded
Code extract:
Rectangle rect = new Rectangle(100,100);
rect.setStyle("-fx-fill:red");
rect.getStyleClass().add("myRectangle");
n.getChildren().add(rect);
scene.getStylesheets().add(NewWorkflow.class.getResource("project.css").toExternalForm());

project.css content:
.myRectangle {
    -fx-fill:blue !important;
}