diff --git a/bndtools.builder/src/org/bndtools/builder/CnfWatcher.java b/bndtools.builder/src/org/bndtools/builder/CnfWatcher.java
index 92fa98087b..08cc961649 100644
--- a/bndtools.builder/src/org/bndtools/builder/CnfWatcher.java
+++ b/bndtools.builder/src/org/bndtools/builder/CnfWatcher.java
@@ -79,6 +79,8 @@ public IStatus runInWorkspace(IProgressMonitor arg0) throws CoreException {
 							MarkerSupport ms = new MarkerSupport(cnfProject);
 							ms.deleteMarkers("*");
 							ms.setMarkers(workspace, BndtoolsConstants.MARKER_BND_WORKSPACE_PROBLEM);
+							// clear errors/warnings, to avoid re-adding
+							workspace.clear();
 						} catch (Exception e) {
 							return new Status(IStatus.ERROR, BndtoolsBuilder.PLUGIN_ID,
 								"error during workspace refresh",