Help with iTunes update and accidentally syncing phone to another iTunes account

I'm really hoping someone can help me.
Earlier tonight I updated iTunes on my laptop. I synced my phone and backed it up only to find an hour later when I was going through my messages that all of my contacts were gone. I read up online and apparently this was a common problem with the new update. I've tried the suggestion of going into settings>icloud and turning my contacts on but my numbers are still gone. When I plugged my phone into my computer again to restore the backup, It automatically started to sync again. I clicked cancel straight away but the previous backup changed from earlier on in the evening to the current time. So now I've no backup from earlier, Just from after I realised my contacts were gone.
I also noticed when I was clicking around that my partners email was signed into the itunes account, not my email. I signed him out and signed myself back in but nothing has returned.
Does anybody have a solution for this? I know I can't use a previous backup because it updated the backup to after I noticed the contacts were gone. I also tried restoring my computer to an earlier time from before I backed up iTunes but there's no recent backups of my computer. I also tried signing into iCloud but theres no contacts there either.
I have a feeling all of this was caused because my partners email was signed into iTunes when my phone backed up but I'm curious as to why it would just delete my contacts and nothing else?

If you have an iPad 1, the max iOS is 5.1.1. For newer iPads, the current iOS is 6.0.1. For the iPad Mini the iOS is 6.0.2. The Settings>General>Software Update only appears if you have iOS 5.0 or higher currently installed.
iOS 5: Updating your device to iOS 5 or Later
http://support.apple.com/kb/HT4972
How to install iOS 6
http://www.macworld.com/article/2010061/hands-on-with-ios-6-installation.html
iOS: How to update your iPhone, iPad, or iPod touch
http://support.apple.com/kb/HT4623
If you are currently running an iOS lower than 5.0, connect the iPad to the computer, open iTunes. Then select the iPad under the Devices heading on the left, click on the Summary tab and then click on Check for Update.
Tip - If connected to your computer, you may need to disable your firewall and anitvirus software temporarily.  Then download and install the iOS update. Be sure and backup your iPad before the iOS update. After you update an iPad (except iPad 1) to iOS 6.x, the next update can be installed via wifi (i.e., not connected to your computer).
 Cheers, Tom

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