Small fix.

lib/core/Project.js

@@ -576,8 +576,9 @@ Project.prototype._restoreNode = function (node, flattened, jsonKey) {
             flattened[key] = local = json;
             local.missing = true;
         // Even if it is installed, check if it's compatible
-        } else if (!local.missing) {
+        } else {
             compatible = this._manager.areCompatible(json, local);
+
             if (!compatible) {
                 // Assign dependants to avoid extraneous warning
                 local.dependants = local.dependants || {};