link :
The --innodb_file_per_table option affects only table creation, not access to
existing tables. If you start the server with this option, new tables are
created using .ibd files, but you can still access tables that exist in the
shared tablespace. If you start the server without this option, new tables are
created in the shared tablespace, but you can still access any tables that were
created using multiple tablespaces.
E sim, um dump e uma restauração são necessários para mover as tabelas existentes para seus próprios arquivos.