Just delete the output. Open the project. Then, on the left, hover on the little down-arrow to the right of the project name, and choose Delete... Delete local album. Then a Make Album will create the album from scratch.
But a simple Make Album should work, even without deleting anything. Just make sure you're not telling jAlbum to process only updated subdirectories, under Album > Settings > Advanced > General. Especially with these JSON-driven albums, that's a terrible option - it needs to process all of the subdirectories.