diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/TaskExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/TaskExecutor.java
index f109e2374aa74c53d3bcaa8c5686094bd528bfad..bd285e63308fce56e7bbe272f0e0b23adf9ec041 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/TaskExecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/TaskExecutor.java
@@ -28,7 +28,6 @@ import org.apache.log4j.Logger;
 import ch.rinn.restrictions.Private;
 import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
 import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.logging.ISimpleLogger;
 import ch.systemsx.cisd.common.logging.Log4jSimpleLogger;
 import ch.systemsx.cisd.common.logging.LogCategory;
 import ch.systemsx.cisd.common.logging.LogFactory;
@@ -133,29 +132,34 @@ public class TaskExecutor
     }
 
     /**
-     * Performs all cleanup task in cleanup-tasks folder.
+     * Performs all cleanup tasks in cleanup-tasks folder.
      */
     public void cleanup()
     {
         Log4jSimpleLogger logger = new Log4jSimpleLogger(operationLog);
         File[] files = cleanupTasksFolder.listFiles(FILTER);
-        for (File file : files)
+        if (files != null)
         {
-            cleanupTask(file, logger);
+            operationLog.info("Perform " + files.length + " clean up task.");
+            for (File file : files)
+            {
+                try
+                {
+                    ICleanupTask cleanupTask = deserializeFromFile(file);
+                    cleanupTask.cleanup(logger);
+                } catch (Exception ex)
+                {
+                    operationLog.error("Couldn't performed clean up task " + file, ex);
+                }
+                file.delete();
+            }
         }
     }
 
-    private void cleanupTask(File file, ISimpleLogger logger)
+    private ICleanupTask deserializeFromFile(File file) throws IOException
     {
-        try
-        {
-            byte[] bytes = FileUtils.readFileToByteArray(file);
-            ((ICleanupTask) SerializationUtils.deserialize(bytes)).cleanup(logger);
-        } catch (Exception ex)
-        {
-            operationLog.error("Couldn't performed clean up task " + file, ex);
-        }
-        file.delete();
+        byte[] bytes = FileUtils.readFileToByteArray(file);
+        return (ICleanupTask) SerializationUtils.deserialize(bytes);
     }
 
 }
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/SegmentedStoreUtils.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/SegmentedStoreUtils.java
index e9f9c247d90b9b4d5ddd8169fba21448337ef4f5..599921c0d988539f61283f72bba68b595349c233 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/SegmentedStoreUtils.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/SegmentedStoreUtils.java
@@ -247,8 +247,8 @@ public class SegmentedStoreUtils
         copyToShare(dataSetDirInStore, dataSetDirInNewShare);
         long size = assertEqualSizeAndChildren(dataSetDirInStore, dataSetDirInNewShare);
         String shareId = share.getName();
-        shareIdManager.setShareId(dataSetCode, shareId);
         service.updateShareIdAndSize(dataSetCode, shareId, size);
+        shareIdManager.setShareId(dataSetCode, shareId);
         deleteDataSet(dataSetCode, dataSetDirInStore, shareIdManager, logger);
     }
 
@@ -276,12 +276,24 @@ public class SegmentedStoreUtils
         }
     }
 
+    /**
+     * Deletes specified data set in the old share if it is already in the new one or in the new one
+     * if it is still in the old one.
+     * 
+     * @param shareIdManager provides the current share.
+     */
     public static void cleanUp(SimpleDataSetInformationDTO dataSet, File storeRoot,
             String newShareId, IShareIdManager shareIdManager, ISimpleLogger logger)
     {
         String dataSetCode = dataSet.getDataSetCode();
         String shareId = shareIdManager.getShareId(dataSetCode);
         String oldShareId = dataSet.getDataSetShareId();
+        if (newShareId.equals(oldShareId))
+        {
+            logger.log(LogLevel.WARN, "No clean up will be performed because for data set "
+                    + dataSetCode + " both shares are the same: " + oldShareId);
+            return;
+        }
         boolean currentIsOld = shareId.equals(oldShareId);
         boolean currentIsNew = shareId.equals(newShareId);
         if (currentIsOld == false && currentIsNew == false)
@@ -292,7 +304,8 @@ public class SegmentedStoreUtils
             return;
         }
         File shareFolder = new File(storeRoot, currentIsOld ? newShareId : oldShareId);
-        deleteDataSet(dataSetCode, new File(shareFolder, dataSet.getDataSetLocation()), shareIdManager, logger);
+        String location = dataSet.getDataSetLocation();
+        deleteDataSet(dataSetCode, new File(shareFolder, location), shareIdManager, logger);
     }
 
     private static void copyToShare(File file, File share)