After a successful upgrade from 11.04 to 11.10 a gradual deterioration occurred -- my laptop became unstable with updates -- I corrected the Aspell file, only to have another appear, I sought but I was blocked out. Had an idea, but resolved one that another problem appeared -- going from bad to worse -- I re-installed windows Vista and Ubuntu 11.10 in the original partitions. Window called it Windows Old and I had no problems recovering my files there - Ubuntu decided it is going to make a new Home directory -- . the questions is where did these files go to after re-installation -- are they deleted? If so That's fine duplicates are in Ubuntu 1 by synchronization - I can only download one file at a time!
I'm not sure exactly what happened based on your description, but there could be a few possibilities. Ubuntu may have formatted your home partition and used it again, in which case the files would be deleted, but might be recoverable with some file recover tool.
Or it may have used a different partition as your home directory, in which case something else could be using that partition, or it could be unused.
Maybe try putting in a live CD and having a poke around all the partitions to look for the files you are after.
Good work on making a backup though! At least you can restore them from the internet.
Not many people could guess that, but you can always check wtih tools that are provided in ubuntu like Disk utility.
You can also help yourself with GParted.
The best way to reinstall is shown in this article. But basically you should always check the order of your partitions with Disk utility and then at install, select "Something else" to set the partitions by hand.