Let me see if I can explain this my wife and I share our office desktop computer (PC) but we both have our own User Accounts. On my wife's User Account I set up iTunes with her own Apple Account and under my User Account I have iTunes set up with my own Apple Account. My wife got an iPad Mini for Xmas and I got an iPad 4 but she decided to return her white one for a black one.
Ok before I sent hers back I backed it up in iTunes to our computer but didn't realize until after I had sent it back I had backed it up in iTunes under my User Account instead of hers. So when I open iTunes under my User Account I not only have my iPad backed up but also her iPad Mini.
I hope this is all making sense since I backed up her iPad Mini in iTunes under my User Account if I restore it from there will it link her iPad to my Apple account? If so it looks like I would be better off setting it up from scratch again.