No your backups arent moved, edited, or deleted when updating, uninstalling, or installing itunes. They are kept in a seperate file. If you want to make a copy of them for safe keeping here's the folder location.
Source: http://support.apple.com/kb/HT4946
The folder where your backup data is stored depends on the computer's operating system. Make sure the backup folder is included in your data-backup routine. iTunes places the backup files in the following places:
- Mac: ~/Library/Application Support/MobileSync/Backup/
The "~" represents your Home folder. If you don't see Library in your home folder, hold Option and click the Go menu.
- Windows XP: \Documents and Settings\(username)\Application Data\Apple Computer\MobileSync\Backup\
To quickly access the Application Data folder, click Start, and choose Run. Type %appdata% and click OK.
- Windows Vista, Windows 7, and Windows 8: \Users\(username)\AppData\Roaming\Apple Computer\MobileSync\Backup\
To quickly access the AppData folder, click Start. In the search bar, type %appdata% and press Return.