I have not used webalizer in awhile, but I think there is an incremental processing feature. This allows you to process multiple log files between the times webalizer backs up the data in its history file.
If you check out the README that comes with webalizer it will tell you how to setup incremental processing.
Making your log files larger just means webalizer has to spend more time sifting through them. Also, this just eats up disk space.
I've stopped using webalizer and now use Wusage for my web stats. Wusage's administration is much easier, especially for multiple sites.
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