My F:\Documents and Settings\User\.spamassassin folder contains my bayes files. I back this whole folder up regularly. Am I right in thinking that if I have backed it up already, I can delete all the .expire files and all old_ files?
Yes
Also, I don't use auto-whitelist, so can I delete that file?
Yes
Also, the user_prefs file is empty because I manage settings elsewhere, can I get rid of this or is it required to have a file there?
Yes, although depending on your SA settings it might get re-created. Spamd does this by default, but there's a command-line parameter that disables it.
Basically I think the only files I need to keep here are: Bayes_journal Bayes_seen Bayes_toks
Is this correct?
Yep.
