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.
this post was submitted on 19 Feb 2025
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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
I just ran into this last night and discovered the solution as well. Unclear why they chose this migration behaviour!
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.