This sounds sort of similar to a problem I had a while back with map data not saving. Do you use cloud storage, and if so how much space do you have left in it?
If I recall correctly, not every world will have a sword shrine, but every shrine will have a sword.
I'm not sure on this much though. Can you send a screenshot so I can see how much is mined?
You may need to make a new world exclusively for this.
Edit: I think you can also get them from the...
What mods do you have on?
I know there's weird stuff that can happen with mods sometimes (ex. Anarchist Mod can sometimes crash game on character creation).
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