Feeds importer imports only some of the nodes
Feeds keep track of previously imported items in the feeds_item table. This also includes items that were only updated by Feeds, but not originally created by Feeds.

Under normal circumstances, when you delete an entity imported/updated by Feeds, Feeds will delete the corresponding import meta data from the feeds_item table. There can be occasions where this does not happen. These are:


During the deletion of the entity, a PHP fatal error occurred which prevented Feeds from cleaning up the import metadata. Non-fatal errors should not cause this, as Drupal would then perform a rollback of the deletion.
Feeds is disabled when deleting the entity.


Feeds doesn't clean up orphaned items from the feeds_item table. To clean this up, you'll need to execute a query on that table. The id column represents the importer ID and feed_nid the feed node ID (the latter is only used when you have attached your importer to a content type and you need to create a node to import content).

Example query to delete all import metadata for the importer 'my_importer':

DELETE FROM feeds_item WHERE id = 'my_importer';

There is an issue to let Feeds automatically clean up orphaned feed items: https://www.drupal.org/project/feeds/issues/1394320

For more information about the feeds_item table, see https://www.drupal.org/node/1768352