There are several reasons why you should consider backing up the PocketPC iPAQ before proceeding to the GNU/Linux replacement:
the operating system replacement is a destructive operation, that will erase everything on the machine
the software that comes pre-installed on the machine is licensed to you (remember you paid for it!), so even if you don't want it, you should keep it as valuable
if you are not satisfied with GNU/Linux, this will be the only way to go back to the original operating system
concerning your own data, remember that you are the only one able to re-create it...
if you experiment on someone else's iPAQ (you probably shouldn't, anyway), you will have to restore everything to its original state
This is why I urge you to backup your iPAQ. When it comes to safety procedure, it is better to have suspenders, a belt, and a parachute than nothing...