I would strongly advise against using Magento connect or downloader to upgrade Magento.
In your example you have downloaded a fresh copy of Magento (system B) I would unzip this into a temp folder and the use rsync to replace all files in system A with those from system B (the upgrade).
I like to use rsync to do this :
rsync -avI –exclude=app/etc/local.xml –exclude=app/etc/config.xml –exclude=index.php –exclude=.htaccess ./magento/ /home/www/magento/
Where /home/www/magento is the path to the 1.9.1.x installation. After copying reset your file permissions
You muse be certain that you have not modified any core magento code, locale or template files as they will be overwritten. I would test the upgrade first on your development system.
When you do this in your live store the process would be
- backup magento db and files
- take store offline i.e. n98-magerun.phar sys:maintenance
- disable cache : n98-magerun.phar cache:disable
- rsync files
- update modman modules (if you use modman) modman update-all --force
- reset permissions
- login to magento
- enable cache
More info here http://blog.gaiterjones.com/upgrade-magento-ce-1-9-1-x-to-1-9-2-0/