Solution – First Step

cd pkginfo
# rm -Rf Mage_All_Latest.txt Mage_All.txt
# cd ..
# sudo -u www-data ./mage upgrade-all
Installing package community/Mage_All_Latest 1.9.2.2
Package community/Mage_All_Latest 1.9.2.2 installed successfully
Starting to download Interface_Adminhtml_Default-1.9.2.2.tgz ...
...done: 1,014,275 bytes
Installing package community/Interface_Adminhtml_Default 1.9.2.2
Package community/Interface_Adminhtml_Default 1.9.2.2 installed successfully
Starting to download Interface_Frontend_Default-1.9.2.2.tgz ...
...done: 747,738 bytes
Installing package community/Interface_Frontend_Default 1.9.2.2
...

Now delete the maintenance.flag file and your shop is updated and online!

Sacado de http://www.fly2mars-media.de/seoblog/magento/magento-1-9-2-2-upgrade-conflict-issue-supee-6788-security-patch-solution-for-this-problem-102558/