Why are there folders from the upgrade site in the production site folder hierarchy?
Oracle Service Cloud sites undergoing the upgrade process
The issue surfaces when an upgrade site (<site>__upgrade) exists, corresponding to a production site installation.
In this case, under %APPDATA%\RightNow_Technologies folder will contain both the production site, and the upgrade one. During the background update process, the folder structure corresponding the upgrade site will be duplicated to the production site folder structure(%APPDATA%\RightNow_Technologies\<site>).
This behavior is the desired one in this situation.
Duplicating the folder structure from the upgrade site to the production one saves bandwidth when the cutover occurs. The binary files for the new version (the upgrade one) are already in place, so re-downloading them is not needed.