diff --git a/MantidPlot/src/ProjectRecovery.cpp b/MantidPlot/src/ProjectRecovery.cpp
index 55c28ab5986b0a4a3366541dbbadf9591dc0f6b4..3534b64ad3645978a6c5c3757d93849c0664773f 100644
--- a/MantidPlot/src/ProjectRecovery.cpp
+++ b/MantidPlot/src/ProjectRecovery.cpp
@@ -355,6 +355,8 @@ void ProjectRecovery::loadRecoveryCheckpoint(const Poco::Path &recoveryFolder) {
 	  // Note: We must NOT throw from the method for excepted failures, 
 	  // since doing so will cause the application to terminate from a uncaught exception
 	  g_log.error("Project recovery script did not finish. Your work has been partially recovered.");
+    this->clearAllCheckpoints();
+    this->startProjectSaving();
 	  return;
   }
   g_log.notice("Re-opening GUIs");