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iTunes can't restore backup but I can find the specific file?

I backed up my iphone last night prior to taking it to apple for repair and what eventually turned out to be a new phone. Then I came home to restore the phone only to have no backups available. I have found the one I want in the "...applecomputer/mobilesync/backup" file but can't get itunes to recognise it. I really only care about 1 specific note as I manually backed up the photos. Does anyone know how to get the full back up or even a targeted back up to happen? Apple help could not help me (after 2hrs of trying). They did say something about older IOS on the old phone and a new IOS on the new phone but couldn't suggest a solution, they could only say they did not know how to get it to sync and that backwards compatibility may be an issue. Thanks