since pdaXii13 is based on beta1/beta3 and build directly on a Zaurus installed with pdaXrom beta1/beta3, it is possible to upgrade those system to pdaXii13 base without reflashing them.
in order to upgrade to pdaXii13 you will need to be running either beta1 or beta3 already and have about 10MB of free space left on your NAND (the exact space needed is not known and may be less).
make sure you do a NAND backup before attempting this. this is a generic upgrade method and may not work as expected on some systems with fancy setups. make sure you have a backup before upgrading to pdaXii13...
What you need to do is download and extract
http://www.tyrannozaurus.com/feed/pdaXii13...ii13-custom.tgz to your Z somewhere (preferably CF card rather than SD card)
Shut down X and any unneeded services including SD service
Then from the extracted directory run
./install-fix-beta3 / upgrade
reboot and your system is patched to the same level as pdaXii13 base.
running
version will tell you which edition and version of pdaXii13 you have.
The full pdaXii13 is available for the C3000 model as a complete install since there is no beta1/beta3 for it in the first place, however, you can use this method to upgrade an older pdaXii13 to the latest patch level as well...
C1000, C3100, C3200 can be upgraded this way without requiring you to reflash, but of course you can use the pdaXii13 Akita installer to flash if you want to.
The installer (both for Alice and Sally) have an upgrade option which basically does the extraction the update file for you and also installs the files.
C7x0, C8x0 can use this method to update their setup.
pdaXii13 base edition is a collection of bug fixes and patches rolled together to fix quite a lot of bugs in pdaXrom beta1/beta3. pdaXii13 full adds a lot of pre-installed and customised applicatons which requires a lot of space and only available to C3x00 models...