If you're assigning new keys on the other end, you'll need to create and store a map of old key to new key during the migration and use it as a lookup when migrating related data.

Hence, the birth of the MySQL InnoDB vs. MyISAM debate. Of course, MySQL users prior to the 5.5 release were probably perplexed by the assertion that the database didn't support foreign keys. MySQL ...

Foreign keys can refer to another column in the same table. The top-level folder might need to be its own parent - I don't know if it'll let you have a NULL there.