In the next development release of ModelConverterX you will find a first implementation of exporting animations to FS2004 scenery MDL files. This item was on the wishlist for quite some time already and I have now given implementing it a try.
I am sure you will find some bugs in this first implementation. Some of my test objects still go wrong, but the majority works fine already. So if you find any trouble or have an object that does not yet work correctly, please let me know.