Raging Seas seems to be wiping out terrain improvements.
Can you clarify what you mean?
if it's cottages, farms and such, I believe that's intentional.
Civ has several different factors determining a tile
1. Terrain. This is plains, grassland, desert, tundra, fields of perdition, etc.
2. Height. This is peak, hills, flatlands, sea
3. Improvement. This includes cottages, farms, lumbermills, etc. Mana nodes are here, and the big unique things like Pyre of the Seraphic are in this category too.
4. Feature. This includes forests, jungles, ancient forests, floodplains, haunted lands, et al.
The most importna thing to consider, as far as I'm aware, is that each tile can contain only one each of the above. You can't have a farm and a cottage on one tile. But you can have a cottage and a forest, because they're in different categories.
That explanation aside, can you clarify what exactly is being removed by the Lanun worldspell that shouldn't be ?