Factory reset will wipe it. Anything synced to iCloud should just download again. If the iPad is set to back up to iCloud then it should redownload all the apps and settings. Photos - will depend on if they are also set to sync to iCloud (or some other service). Same with Music - where did it come from...
It's normal for it to disappear from the Finder during an update for a couple of minutes though, but you usually see a progress bar on the screen of the device as this part happens.

