Lists are a very old and very buggy section of the site. Try going to the list, at the top is a section marked tools. It has 2 options, run them in reverse order (ie run the bottom one first and then the top one) and it will try to rebuild your list.
It is good to know that the life list is not built up in real time and behaves like a cache that needs to be refreshed. Whether or not it should be like this is another question (I think it could remain like that).
This fixed the issue, regenerating the life list:
Now I don’t have “Rupicapra rupicapra” anymore in my life list.
It’s not designed to be a cache, it is designed to be real time and dynamic, it just is very buggy. This should also fix your other post about the wrong date.
Regarding your other flag, from the above note, it is not clear if you ran both steps under the tools menu, or just the 2nd and stopped when it seemed to resolve. You need to run both, and as I noted in reverse order for the updates to fully generate.
You can also manually add species to your life list, so it intentionally doesn’t remove species. As far as I’ve seen, the system doesn’t distinguish between species you manually added and those from observations, including where the ID changed.