diff --git a/lib/core/Project.js b/lib/core/Project.js
index 3f4933a3..b897aaba 100644
--- a/lib/core/Project.js
+++ b/lib/core/Project.js
@@ -649,16 +649,21 @@ Project.prototype._walkTree = function (node, fn, onlyOnce) {
 };
 
 Project.prototype._restoreNode = function (node, flattened, jsonKey) {
-    // Do not restore if already processed or if the node is
-    // missing or incompatible
-    if (node.dependencies || node.missing || node.incompatible) {
+    var deps;
+
+    // Do not restore if the node is missing or incompatible
+    if (node.missing || node.incompatible) {
         return;
     }
 
-    node.dependencies = {};
+    node.dependencies = node.dependencies || {};
     node.dependants = node.dependants || {};
 
-    mout.object.forOwn(node.pkgMeta[jsonKey], function (value, key) {
+    deps = mout.object.filter(node.pkgMeta[jsonKey], function (value) {
+        return !node.dependencies[value];
+    });
+
+    mout.object.forOwn(deps, function (value, key) {
         var local = flattened[key];
         var json = endpointParser.json2decomposed(key, value);
         var restored;