The iTunes Store community is really for issues with the iTunes Store rather than iTunes in general or device specific topics. I asked for the thread to be moved. The grayn280 warning seems to result form an occasional forum time out error, it can be ignored, but if you've taken a long time composing it may best to copy your post, or check you are signed in from another tab, just in case.
In the meantime see Recover your iTunes library from your iPod or iOS device if there is content on the device that isn't in your library. You don't want to be in that position.
Perhaps if had been dealt with at the time it first happend then method in Empty/corrupt iTunes library after upgrade/crash might have proved useful. Somewhere along the line it seems iTunes no longer sees the current library as the home library for the device, and it may be as easy now to move forwards as backwards.
If all of the content that is on your device is already in your library that the warning isn't so serious. Erasing and reloading may take some time, but it should be a one time hit.
tt2