iphone synced to another library.

I rarely plug my phone into the computer but today I needed to do a backup and restore to fix a problem with my wifi and also voicemail. I wanted to transfer purchases to the computer but could not. I clicked on manually manage and received the message that the phone was synced to another library and that if I proceed my content will be erased. I have many apps that I don't want to lose. Now after the restore all the apps are having to download from the store and some apparently no longer exist let alone the fact that its taking forever to do. The phone has never been connected to any other computer. any ideas?