I had expected to see the updated values in the morning, but instead I was greeted by a non-responding EBT website. I had an open shell session to the server, and here's what I managed to see after waiting a few minutes while the server processed the command:
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[anssi@tiikeri anssi]$ uptime
10:44:03 up 80 days, 18:19, 3 users, load average: 686.66, 678.24, 660.45
The load averages shouldn't be that high.. MySQL had pretty much died while processing the maintenance queries. Looks like some of the design choices that were made about 4 million notes ago don't really scale well to the current situation. After rebooting the server things started working again. Sorry for the interruption, I guess I'll need to rewrite some of the scripts to make the database load a bit lower.