I am not sure if this is your problem, but sadly you can not safely migrate assets with other structure folder than the original, because you probably will get lot of errors. You need first to migrate the content with the same folder structure, eg: Content/JcInventory/… and then you can move the folder inside your project. After that , you must have a carnal fight with redirects and “dirty empty” folders everywhere that you cant delete .
@Staggerlee: great news about the update 