Janine,
I think it's the "history" file you should remove or, rather, rename and keep around for a bit since I'm not totally sure. It should be found in the -o output dir, or in the current directory (~/nsadmin ?) if the -o option has been omitted.
Have a look at the proc that I recently submitted to new-file-storage:
https://openacs.org/new-file-storage/download/acs-webalizer-init.tcl?version_id=594
It incrementally processes all the rolled logs I have in a certain dir, which of course may be wasteful because it does it every night and I keep 5 log files around... However it should be easy to change the "bash" FOR loop to suit your needs.
Good luck!
