but would that not mean that the bayes filter will learn the headers that spam assassin adds as spam .. and then after a while only start classing mail that already has the spam headers as bayes_99 ?
I really do not know, I am just asking.
Erm.. no. Bayes doesn't even examine SA's own headers, so it won't learn from that.. ever.
SA's bayes would also be absurdly broken if something like that could shake up the classification.. Bayes is VERY robust. It's not uncommon for messages to hit over 30 different bayes tokens. The state of just one token is pretty much a non-issue for bayes. One addball won't overthrow a dozen others.