When trying to filter by this custom field (for all it's values) I cannot see any tickets, though they are definitely a lot that answer this query's criteria.
When I updated the field (using the edit option) I could suddenly see it by filtering the new value.
Returning it to the old value works - now I see only the one ticket (but I have thousands).
re-indexing was made - didn't help. Any thoughts? How can I make JIRA see this field?!
I'm not sure I understand the problem. Could you give us the searches you have tried and explain what is wrong with them?
The JQL is what we need - if you're using simple search, then you can still get the JQL - run the search, get the "broken" result and then click "advanced" and it will display it as JQL for us
But that's not what you've said - you've described behaviour that works. That's why I am lost. The other question I have is what you mean by "manually update the issue"? Editing the version IS updating the issue. That suggests that you are trying to update the version with something you've scripted, and got wrong...
So how do you put it into a "broken" state? A field change IS an edit, but you say that fixes the problem, so we need to know how you are getting it broken. What process is breaking it? We need to find out what is broken in your edit process because it's not indexing in the way it should.
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