[Trent Adams]

As long as you have your plugins in /my-plugins/ and your template folders in /my-templates/ then you should be able to go and just overwrite the files from the download into your bbPress folder. The download files don’t have the things you need to protect:

.htaccess

config.php

/my-plugins/

/my-templates/

As long as all your changed files are in the folders, you can go ahead and upload!

Trent