You shouldn't replace the Tilesets inside the Data folder. You should create a Tilesets subfolder inside the folder of your level (inside Worlds) and put your own Tilesets there: that way they'll override the default Tilesets with the same number, but only for your level, and, more importantly, when you export the level (.knytt.bin) they'll be added automatically.
This goes for custom Ambiance and Music as well.