Versions 1.9.9 and newer can be upgraded. Use the web interface to log in to your IPCop and take a backup on a floppy, USB key or downloaded files using the Backup Administrative web page. If you don't know how to do this, please read the IPCop Administration Manual section entitled System->Backup AW. During installation you will be asked whether you wish to restore your settings from a backup floppy or USB key.
There is no upgrade path from IPCop 1.x to IPCop 2.0.0. Migration of individual pieces is described in HowTos.