The routine I'm doing calls for running both with and without Honorbuddy - I do some stuff manually, then launch Honorbuddy for a while, then I need to do stuff manually again. Would it be safe to attach/detach Honorbuddy like that all day long or would it be better to restart WoW as well? Keeping Honorbuddy on pause is not an option because my RAM is pretty low for that.
You should be fine - I don't see why there would be any issues at all, i do this all the time never had any issues.