Help with iPod Touch in recovery mode

I am trying to help my sister with her daughter's iPod touch. The end goal is to update to iOS6. It is a fourth gen iPod Touch. I plugged it into iTunes (iPod was still iOS V4.something or other) and it said there was an update availalbe. I clicked Download and Update. Got a message about the update deleting all the apps since this iPod had been synced with another computer (my sister has a new computer since she last synced the iPod -- the old computer is no longer available). I cancelled out of the update and did a transfer purchases and then backed up the iPod. I then started the iOS 6 update again. It downloaded the update and then it said "backup up iPod." At that point I left so I don't know what happened after that but it is now saying that iTunes has detected an iPod in recovery mode. My question is this: if we let it do the restore (which is the only option), will I be able to go back into iTunes and restore from the backup that I took MANUALLY (not the backup that it did as part of the iOS 6 update)?

Thanks.

Lisa