Are there any critical files, like some kind of root index file

Nope. There _might_ be some oddness if FID 100 and FID 110 don't exist, but emplode should recreate these if necessary.

And, as you say, this shouldn't affect the soup views in emplode at all. emplode downloads a list of the tunes available, and then laces them together into playlists. Searches just apply to the list of tunes.