After spending time getting a DNS server running in the lab at home I end up stuck here. I'll probably just skip the upgrade and re-install the new version, but on the off chance there's an easy fix to this I thought I'd post it. I'm able to get the log bundle from the web admin side of my current vcsa, so I know it works. Not sure what the migration tool might be doing that prevents it from getting the logs. Not even sure why it's necessary. I've unchecked the box for performance data migration just in case that was it, but it didn't make any difference.
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