Hmm... yes the modules you've added will not be included.
If you just replace some folders or files on your server like your theme or some modules, it will not have any impact on your data. You will keep customers, addresses and orders because they are stored in your database and changing those files will not touch at the database.
Anyway, to restore your files, you must have a backup. If you have absolutely no backup, you will not be able to restore anything. So you have to find a backup of the files of your shop.