ocamlwiki seems to be a LLM-filled website. I would encourage you to avoid it, see this discussion: What's up with ocamlwiki?
as for this, this is pretty simple. The file mentioned above was somehow removed (how is the mystery) and opam update simply redownloads the repository and sync it with what you have locally so in this case it saw that the file was missing and copied it back.
Could you submit a bug report in the opam bugtracker with the result of opam config report and the output of the failing command?
Given another user reported a similar issue a few days ago on here I’m wondering if there are something in common between you two. cc @dromas