There are many unanswered questions in this scenario. Have you checked that the folders haven't been moved, perhaps into the Ubuntu One folder? If deleted, you may have to use file recovery software such as 'foremost' to recover your files. Foremost can be run from the command prompt and with the -t switch can be set to only look for certain file types. The general syntax is: foremost -t (filetype to find) -i (input, or disk to be searched) -o (output, or destination for found data)

So for example if you wanted to search disk B for lost jpeg files and store the recovered data on a third disk the command might resemble:
foremost -t jpeg -i /dev/sdb -o /dev/sdc/folder

As for remastersys running, it's supposed to make a backup of your system as an iso file. Did you have it running for a reason, perhaps on a schedule? If so you might be able to mount a recent iso and copy your files out of there.