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If you’re playing in a private browsing mode, saving will not work. If it’s not that, it may that Safari has a limited storage space (about 5MB last I checked) for websites and web apps to use, and it deletes content that isn’t used after only one week if the user hasn’t been to those sites. If the 5MB of storage is full, it may delete content even sooner. How it chooses what to delete isn’t clear to me, but I suspect it’s a combination of how often you visit/use a given website or web app and how recently you’ve used it. So my recommendation is:

  1. Make sure you aren’t in a private browsing mode.
  2. Make sure to open the game occasionally so Safari doesn’t delete it.

There are some improvements I may be able to make on my end to help alleviate these issues, like letting users copy and paste saved data as text instead of passing them around as files, but these ideas are still in their infancy for right now.