Music missing after iOS update.

After updating the OS on my iPad mini all the songs I had burned from my cd collection are missing from my itunes library. The songs purchased from iTunes are still there. The burned songs still exist on my wife's iPad mini which I haven't (and won't) update. My home PC runs windows and when I triedto sync the updated iPad with iTunes the songs were deleted from the PC as well (and they're gone from iCloud too).

My four questions are why did this happen, how can I prevent it happening again, can I manually make a backup copy the complete iTunes library on the un-updated iPad, and is there anyway to get the songs from one iPad to another.

Thanks