diff --git a/pillar/cli.py b/pillar/cli.py
index db004f5d..62f5da7f 100644
--- a/pillar/cli.py
+++ b/pillar/cli.py
@@ -697,6 +697,7 @@ def upgrade_attachment_schema(proj_url=None, all_projects=False):
     def replace_attachments(project):
         log.info('Upgrading nodes for project %s', project['url'])
         nodes = nodes_coll.find({
+            '_deleted': False,
             'project': project['_id'],
             'node_type': {'$in': list(nts_by_name)},
             'properties.attachments': {'$exists': True},