Let file.index be the index in post.files and file.docIndex be the index in the document.

src/classes/Post.Clone.coffee

@@ -45,7 +45,7 @@ Post.Clone = class extends Post
       file = {}
       for key, val of originFile
         file[key] = val
-      fileRoot = fileRoots[file.index]
+      fileRoot = fileRoots[file.docIndex]
       for key, selector of g.SITE.selectors.file
         file[key] = $ selector, fileRoot
       file.thumbLink = file.thumb?.parentNode

src/classes/Post.coffee

@@ -172,9 +172,11 @@ class Post
   parseFiles: ->
     @files = []
     fileRoots = @fileRoots()
-    for fileRoot, index in fileRoots
+    index = 0
+    for fileRoot, docIndex in fileRoots
       if (file = @parseFile fileRoot)
-        file.index = index
+        file.index = (index++)
+        file.docIndex = docIndex
         @files.push file
     if @files.length
       @file = @files[0]