Formatting issue with Time Machine backup files

[revtmk]

I have a 3TB Laci thunderbolt external that I'm using for Time Machine backup. The drive has one large partition (about 2.5T) formatted 'Mac OS Extended (journaled) that I intended to use as the iMac backup in our office. The other smaller partition was going to be backup for files from an older PC. However, I just discovered that a wrong selection was made for Time Machine and it has been backing up to the smaller partition, which it has formatted as 'case sensitive'. I can't move the backup from one partition to the other because of the different formating. How can I move these files to some other disk, reformat the Lacie, and then move them to the correct partition? Thanks!