Looks like all operating system files are on ROM and load into RAM when necessary and released from RAM when you finish using them.
Casio pocket pc has a secondary battery to support the RAM when you exchange for a new main battery. Ipaq doesn't.
CF card is like a hard drive. The data stays there even there is no power supply. Ipaq's flashable ROM is kind of the same. But you cannot use your Pocket PC to make change to it. You have to use the software utility supplied by compaq to update it.
Your file will be on RAM. You mustn't use iPaq until the battery is gone. You cannot replace the battery in iPaq since it is built-in battery, Li Polymor. You have to re-charge battery when there is a warning. If you don't do it within 24 hours, your data will be gone.