Is the second partition NTFS? If so, don't delete anything with Knoppix. You risk completely corrupting the partition, not just the other files there but any files that you might try to recover.

I suggest instead using Knoppix to back up files to another computer across a network, or to back up to a flash drive or other FAT partitioned device. And, with some versions of Knoppix you'll have to be sure that you mount the partition with read-write access. Just don't do that do a NTFS partition.