Hi!
I'm sorry you're having issues with the saving functions. Unfortunately the save to disk and load file function is a javascript add on coded by a third party so I have little control on how it works. The Twine format I use (Harlowe) doesn't have a save to disk function originally and I found this add-on on GitHub. The person making it has been kind enough to update it to the best of their ability has Harlowe gets updated, but it might still have some compability issue.
If I ever find a way to have more reliable saves in the future, I'll make sure to implement it. As of now, the best advice I can give is to play the game on desktop or laptop, use the cookies saves, and make sure the cookies aren't regularly erased by your browser. Mobile devices seem to erase cookies regularly no matter what you do.