I just ran into this last night and discovered the solution as well. Unclear why they chose this migration behaviour!
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I'm just running into this now. It also won't let me log into the web interface. I'm glad I experimented with a second install before upgrading my primary pihole.
I made sure to read about their changes and still ran into this issue. All I found was a forum post from the beta, so it was clearly something people would be affected by. Finding out what was wrong was easy but finding that command was not.
I went through the same process as you. They clarified the issue three days after release though https://pi-hole.net/blog/2025/02/21/v6-post-release-fixes-and-findings/#%3A%7E%3Atext=your%C2%A0local%C2%A0network.-%2CCustom%2Cconfigs+not+loading%2C-Sorry%2C+this+probably