Phillip Wood wrote:

We should be removing the entry entirely if the user removes it from the
todo-list see b3b1a21d1a (sequencer: rewrite update-refs as user edits
todo list, 2022-07-19) where the commit message says

1. If a '<ref>/<before>/<after>' triple in the update-refs file does not
   have a matching 'update-ref <ref>' command in the todo-list _and_ the
   <after> value is the null OID, then remove that triple. Here, the
   user removed the 'update-ref <ref>' command before it was executed,
   since if it was executed then the <after> value would store the
   commit at that position.

I think that is the best approach but it seems the implementation isn't
actually doing that.

Thanks for pointing this out. This approach seems to have only been applied
to 'git rebase --edit-todo', so ideally the fix will just be "do the same
thing in the initial rebase."

I got sidetracked yesterday and didn't get as much time to work on this as
I'd liked, but I should be able to send a patch today.