Here's the story:
These issues that were hidden have some things in common:
Anyone knows something about that?
Presumably, they were created, but never indexed, and so a JQL search wouldn't find them because the search methodology depended upon an index referencing the issue. Once you re-indexed the project, they started showing up in search results.
I can't explain why they were not index upon the original creation, you'd likely have to check JIRA logs around the time of the creation to dig into that.
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