you can start from checking where it comes from:
grep 'class="header links"' ./app/ ./vendor/ -r
grep '<!-- Account Links' ./app/ ./vendor/ -r
grep 'MENU BLOCK NAME ID' ./app/ ./vendor/ -r
and use other search variations.
there are few options:
- extra line in layout
- layout reference for links in block mixed
- other extension injects own menu
- multiple themes installed and static files deployed from them
when you install magento , go to github and create repository, push your files.
every change you push to github, then you can see it in history.