You can't restore a database by simply loading in the contents of the database directory. InnoDB stores other information in some master files located in the main MySQL data directory.
The only reliable method of recovering all data is to either use a mysqldump
and restore procedure, or to FLUSH WITH WRITE LOCK
before copying the entire contents of the MySQL data directory. This method is not recommended for production systems as it locks the entire database for the duration of this operation.