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).
I went through the steps that you suggest with a test copy and that’s exactly what’s happening. Twine isn’t saving updated name to the story file listing even though the file itself is saved with a new file name. But if you rename it and then trigger a save by editing a single passage, it’ll update the file name listing correctly.
I also found that when you restart twine and the file name is the same as the old file name, rename it to the new file name again. It’ll throw an error saying that the .html file doesn’t exist. Ignore that. It’ll now have the story listing pointing at the right file and you’ll be able to edit again. Just be sure to go into the story and edit a passage to trigger a save. It’ll now update the listing correctly without creating a duplicate file.
This seems like a really simple fix to me, which is basically just forcing Twine to update the file listing when you rename, which is what it should have been doing all along.
If it were just the one bug report, I’d suggest letting HiEv or someone else do it. But I see that you have more than one, so I’m not sure. I’m fairly new to this forum so I don’t know whether or not it’s a good idea to clog it up with bug reports that should really be on the repo instead of here.
For what it’s worth, I originally created my github account only for submitting bug reports. It wasn’t until recently that I used it for my own project.
@tayruh Thank you for re-testing the renaming-issue.
And I wil consider the github account. I am completely new here myself. Working with twine for 3 months now.