How to skip (not ignore) some rows in migration?
Migrate doesn't work with attempts, so it always performs one migration (that you can update with the latest content). 

Considering the fact you need some parent do be defined first, it might be easier to apply some sorting, so the parent is always created before the child (and you would not need several attempts). If you are migrating from a Drupal (7) site you can use the menu_links table for this. See the section about book hierarchies here: Migrating Book module nodes for a similar situation.

If you are not migrating from Drupal, but some other system you might want to look for a similar table.

As an alternative, you might be able to use the handleSourceMigration() function to see if the old parent id is already migrated (function returns NULL otherwise) and skip rows based on that, then re-run the migration. But I have never used this method and it might not work.