diff --git a/js/core.js b/js/core.js
index 2e42f3e6..b6835e49 100644
--- a/js/core.js
+++ b/js/core.js
@@ -556,6 +556,21 @@ define(
 			});
 			version = "v2";
 		}
+		
+		// Upgrade from v2 to v3
+		if(version == "v2") {
+			var fileIndexList = _.compact(localStorage["file.list"].split(";"));
+			_.each(fileIndexList, function(fileIndex) {
+				if(!_.has(localStorage, fileIndex + ".sync")) {
+					localStorage.removeItem(fileIndex + ".title");
+					localStorage.removeItem(fileIndex + ".publish");
+					localStorage.removeItem(fileIndex + ".content");
+					localStorage["file.list"] = localStorage["file.list"].replace(";"
+						+ fileIndex + ";", ";");
+				}
+			});
+			version = "v3";
+		}
 		localStorage["version"] = version;
 	}
 	// Setup the localStorage when starting
diff --git a/js/file-manager.js b/js/file-manager.js
index 902fc76f..e4ed4c6f 100644
--- a/js/file-manager.js
+++ b/js/file-manager.js
@@ -89,17 +89,17 @@ define(["jquery", "core", "synchronizer", "publisher", "underscore"],
 
 		// Remove synchronized locations
 		var syncIndexList = _.compact(localStorage[fileIndex + ".sync"].split(";"));
-		localStorage.removeItem(fileIndex + ".sync");
 		_.each(syncIndexList, function(syncIndex) {
 			fileManager.removeSync(syncIndex);
 		});
+		localStorage.removeItem(fileIndex + ".sync");
 		
 		// Remove publish locations
 		var publishIndexList = _.compact(localStorage[fileIndex + ".publish"].split(";"));
-		localStorage.removeItem(fileIndex + ".publish");
 		_.each(publishIndexList, function(publishIndex) {
 			fileManager.removePublish(publishIndex);
 		});
+		localStorage.removeItem(fileIndex + ".publish");
 
 		localStorage["file.list"] = localStorage["file.list"].replace(";"
 			+ fileIndex + ";", ";");