According to the official git doc, the following command should do the magic:
$ git add -u
Now, you must be thinking that the question was asking for ways to "remove multiple deleted files", how add command will do, right? Well, let me explain.
-u or --update will update the index just where it already has an entry matching <pathspec>. It will remove as well as modify index entries to match the working tree, but adds no new files. If no <pathspec> is given when -u option is used, all tracked files in the entire working tree are updated (old versions of Git used to limit the update to the current directory and its subdirectories).