diff --git a/lib/parser/pbxproj.js b/lib/parser/pbxproj.js
index f5c71d3..4112af1 100644
--- a/lib/parser/pbxproj.js
+++ b/lib/parser/pbxproj.js
@@ -178,9 +178,47 @@ function peg$parse(input, options) {
       peg$c6 = function() { return Object.create(null) },
       peg$c7 = function(list) {
               var returnObject = list[0][0];
-              for(var i = 1; i < list.length; i++){
+
+              for (var i = 1; i < list.length; i++) {
                   var another = list[i][0];
-                  returnObject = Object.assign(returnObject, another);
+
+                  /*
+                   * Ensure previously parsed section entries are not lost
+                   *
+                   * Example:
+                   *
+                   * If "returnObject" contains:
+                   *
+                   *  {
+                   *      PBXTargetDependency: {
+                   *          'A': {},
+                   *          'A_comment': 'PBXTargetDependency'
+                   *      }
+                   *  }
+                   *
+                   * And "another" contains:
+                   *
+                   *  {
+                   *      PBXTargetDependency: {
+                   *          'B': {},
+                   *          'B_comment': 'PBXTargetDependency'
+                   *      }
+                   *  }
+                   *
+                   * Using "Object.assign(returnObject, another)" would lose
+                   * "A" as it would replace the entire PBXTargetDependency.
+                   *
+                   * Instead, we will merge each top-level property of the
+                   * objects, if it exists and is an object else add.
+                   */
+                  for (var key in another) {
+                      returnObject[key] = (
+                          returnObject[key] &&
+                          another[key] &&
+                          typeof returnObject[key] === 'object' &&
+                          typeof another[key] === 'object'
+                      ) ? Object.assign(returnObject[key], another[key]) : another[key];
+                  }
               }
               return returnObject;
           },
diff --git a/lib/parser/pbxproj.pegjs b/lib/parser/pbxproj.pegjs
index 9897048..f93faed 100644
--- a/lib/parser/pbxproj.pegjs
+++ b/lib/parser/pbxproj.pegjs
@@ -17,18 +17,6 @@
     under the License.
 */
 
-{
-    function merge_obj(obj, secondObj) {
-        if (!obj)
-            return secondObj;
-
-        for(var i in secondObj)
-            obj[i] = merge_obj(obj[i], secondObj[i]);
-
-        return obj;
-    }
-}
-
 /*
  *  Project: point of entry from pbxproj file
  */
@@ -60,9 +48,47 @@ AssignmentList
   = _ list:((a:Assignment / d:DelimitedSection) _)+
     {
         var returnObject = list[0][0];
-        for(var i = 1; i < list.length; i++){
+
+        for (var i = 1; i < list.length; i++) {
             var another = list[i][0];
-            returnObject = merge_obj(returnObject, another);
+
+            /*
+             * Ensure previously parsed section entries are not lost
+             *
+             * Example:
+             *
+             * If "returnObject" contains:
+             *
+             *  {
+             *      PBXTargetDependency: {
+             *          'A': {},
+             *          'A_comment': 'PBXTargetDependency'
+             *      }
+             *  }
+             *
+             * And "another" contains:
+             *
+             *  {
+             *      PBXTargetDependency: {
+             *          'B': {},
+             *          'B_comment': 'PBXTargetDependency'
+             *      }
+             *  }
+             *
+             * Using "Object.assign(returnObject, another)" would lose
+             * "A" as it would replace the entire PBXTargetDependency.
+             *
+             * Instead, we will merge each top-level property of the
+             * objects, if it exists and is an object else add.
+             */
+            for (var key in another) {
+                returnObject[key] = (
+                    returnObject[key] &&
+                    another[key] &&
+                    typeof returnObject[key] === 'object' &&
+                    typeof another[key] === 'object'
+                ) ? Object.assign(returnObject[key], another[key]) : another[key];
+            }
         }
         return returnObject;
     }