iTunes forgot about my iPhone...?

Yesterday I was changing some preferences in iTunes, I turned on home sharing and deleted all but the latest backup for my iPhone and iPad. Shortly later I tried syncing my iPhone and iTunes acted like it never saw my iPhone before. Asking to restore from backup or setup as a new phone. I did the setup as new because I dont like restoring backups to keep my phone as clean and running as smoothly as possible. I have had issues in the past the followed the restore so I dont use it. The problem now is that even though it is the same library and all, nothing is selected to sync. I have so many apps and just spent so long installing all of my apps, logging into everything and moving the icons to where I want them on my 4S. Even though iTunes sees the order of my apps currently installed, if I check the app to sync it again it looks like it will reinstall it and will not be where I put the icon, removing all of my folders. My iPad however works fine and syncs as normal. Anyone know why this would happen and if there is any way to fix this without loosing all of my settings, and not restoring from a backup?

Thanks for any help you can provide...