I'm not sure what files it would be deleting other than files it needs to in order to install the updated version. It won't touch your photos! And when I updated mine, it left all my presets and customizations in place also. So I doubt you have anything to worry about by updating. In fact, you have much to gain because there was a significant improvement in how LR handles memory put in place in release 2.3.
I updated mine a while back - no problems. Didn't touch images or presets. A lot of these "updates" I use such as for AVG, ZoneAlarm and others go thru an uninstall first, then complete the new install.
I believe this affects stuff in c:\program files and not so much the files/data that are stored in Documents and Settings.