diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java
index b939d37..51ee9e9 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java
@@ -759,12 +759,14 @@
 			}
 		} else {
 			FileUtils.delete(packedRefs, FileUtils.SKIP_MISSING);
-			FileUtils.delete(headFile);
-			FileUtils.delete(logsDir, FileUtils.RECURSIVE);
-			FileUtils.delete(refsFile, FileUtils.RECURSIVE);
+			FileUtils.delete(headFile, FileUtils.SKIP_MISSING);
+			FileUtils.delete(logsDir,
+					FileUtils.RECURSIVE | FileUtils.SKIP_MISSING);
+			FileUtils.delete(refsFile,
+					FileUtils.RECURSIVE | FileUtils.SKIP_MISSING);
 			for (String r : additional) {
 				new File(getDirectory(), r).delete();
-		}
+			}
 		}
 
 		FileUtils.mkdir(refsFile, true);