When my itunes broke because it got out of step with the quicktime version (itunes was a later version than quicktime, and it wouldn't run, crashed immediately after starting it every time) I had to reinstall it. Nothing was synching by default so I had to go through all the sync settings again to put them back to how they were on the previous install. When I first synched itunes removed everything from my phone which sounds like what you're experiencing. After I reset all the synch options all my apps and music were copied back to the phone (including some I had deleted from the phone earlier, but had synched with itunes previously)
I think I also had to deauthorise my itunes account and then authorise it again for the new itunes instance. Might be worth doing that too.
Last edited by jtnz; 01-16-2012 at 3:12 PM.