I suspect that there may be a bit of rust binding the spindle to either bearing. If you're replacing the BB anyway you have the ption of getting a bit rough with it. Take your wooden mallet and give it a more persuasive shot. soaking the gap between the bearing and race on both sides with penetrating oil and waiting 24 hours will also help.
If it were mine, and being impatient. I'd give it one or two good blows now, then use penterating oil and come back if that didn't work.
BTW-since you want to preserve the spindle, thread the end bolt back in and bottom it so you're striking solid material, not a thin tube, nor is the impact stressing the threads.
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