Jira users is the standard one, but you need to check the global permissions page to see if there are others, and don't forget Admins can always log in even if they are not in jira-users. That begs the question of what you mean by "missing users". Why are you running these queries - what exactly is the problem here?
Because we don't actually know what to do - your data is not understood, so it's pointless trying to do anything other than investigate that. If you need to do this without understanding the data, then the only safe option is to use the gui. If you are determined to do this with SQL, then you need to establish what data to change properly, not just randomly hope something might work.
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