Twine Version: 2.3.5
Story Format: Harlowe 3.1.0
There are several postings and issues about problems with story management when stories are renamed.
https://github.com/klembot/twinejs/issues/615 and …/639, …/644
I had the same kind of problem, tested it, and came to this conclusion:
Possibly these bugs happen because a story is not saved immediately (with its new name), after it was renamed.
The renamed story is only saved, when, after renaming, one edits a passage. If I leave twine without editing a passage, the renamed story is not saved, so there exists nor story with the new name on hard disk (under Windows10 it is in …<user>\Documents\Twine\Stories).