Generally speaking, installing Red Hat Linux over a prior installation (including Red Hat Linux) will destroy some and often all the data on the disks (virtual and physical) attatched to that Logical Partition (LPAR). If these disks contain data which is important to you, the data should be protected. There are a variety of ways to do this, some of which are unique to the iSeries environment.
The data can be saved and removed from the system before the (re)installation. This would be the ordinary and traditional Linux means of preserving data (tarballs, etc.).
Moving or copying the data (via FTP, NFS, etc.) to another Logical Partition, either OS/400 or Linux. Since each iSeries Logical Partition is independent, one Logical Partition's data is unaffected by a reinstall in a different Logical Partition.
Removing the disks from the Logical Partition during the installation. If your Red Hat Linux installation contains more than one disk (virtual or physical) and that disk does not contain data from the Red Hat installation (e.g. is mounted at /home/myuserid, mounted as the directories containing the data base data) it can be removed from the Logical Partition for the duration of the reinstall, and then added back in after the installation is complete. See the Configuring Linux in a Guest Partition document (http://publib.boulder.ibm.com/pubs/html/as400/v5r1/ic2924/info/rzalm/rzalmlinuxkickoff.htm) for details on how these functions are performed.
Adding disks, copying the data, and then removing the new disks during the installation. If you have data to spare on an OS/400 partition, creating a new virtual disk, mounting it, copying the data, and then removing it during the installation is another way of obtaining the benefits of step 3, even if you did not initially plan for it. After the installation, the disk can be added back and permanently mounted, or simply copied back and the new disk deleted. A similar procedure could be used for a spare physical disk.