Manual PS3 System Update.?

I know how to manually update the system, i did on another hard drive than the one i use in the system. My question is, if i do it on my main PS3 drive, would i lose all the DLC content, games i downloaded through the store, my other users and the content from their store page and my custom configurations, including paired headphones, controllers, and every other thing that isn't connected, downloaded or installed during software update?