diff --git a/src/java/org/apache/cassandra/db/DefsTable.java b/src/java/org/apache/cassandra/db/DefsTable.java
index d564eafa11..88d184e32c 100644
--- a/src/java/org/apache/cassandra/db/DefsTable.java
+++ b/src/java/org/apache/cassandra/db/DefsTable.java
@@ -323,6 +323,8 @@ public class DefsTable
             // store deserialized keyspaces into new place
             dumpToStorage(keyspaces);
 
+            flushSchemaCFs();
+
             logger.info("Truncating deprecated system column families (migrations, schema)...");
             dropColumnFamily(Table.SYSTEM_TABLE, OLD_MIGRATIONS_CF);
             dropColumnFamily(Table.SYSTEM_TABLE, OLD_SCHEMA_CF);
diff --git a/src/java/org/apache/cassandra/tools/StandaloneScrubber.java b/src/java/org/apache/cassandra/tools/StandaloneScrubber.java
index 813ccd2a43..481406fc8c 100644
--- a/src/java/org/apache/cassandra/tools/StandaloneScrubber.java
+++ b/src/java/org/apache/cassandra/tools/StandaloneScrubber.java
@@ -55,7 +55,9 @@ public class StandaloneScrubber
         Options options = Options.parseArgs(args);
         try
         {
-            Directories.migrateSSTables();
+            // Migrate sstables from pre-#2749 to the correct location
+            if (Directories.sstablesNeedsMigration())
+                Directories.migrateSSTables();
 
             // load keyspace descriptions.
             DatabaseDescriptor.loadSchemas();