Tough to give a straight answer without knowing more about your environment.  I would say though, that anything you are going to do will be much easier if you have a local development environment to do it in.

If you are running a compiled copy of DNN(which you probably are) you will be able to open it in VS as website.  I would then suggest creating a new VS Web Application Project, deleting everything out of it, and adding all of the broken module's source files. 

Once you can get DNN into Visul Studio, you can use the instructions in this blog post to debug modules.

 The .dnn file that VS doesn't recognize is called a manifest file.  It is in XML format and contains instructions to DNN about how to install the module(Filenames, locations, module details, etc).  Unless you changed it, and then reinstalled the module, this is not causing your problem.