Hi, I think the problem is that you've got so many messages and it will take a long time for Mail to scan your messages and apply the rules. I've done this before with a few thousand messages and I too thought nothing was hapenning for a long time. I can't imagine what it would be like with 48 thousand. So, my advice, after you try applying rules, press command-option-0 to view Mail activity. Take a look and see if Mail is doing anything. If it is, then just give it time. If not, then let us know and maybe someone will have more ideas.
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