I'm sorry, I can't understand most of this.
I understand the main problem: You have issues that do not appear on the dashboard but do appear when you search for them.
There's not enough information here though. What part of the dashboard? Most of the stuff on the dashboard runs from filters, so the most likely explanation is that the filter on the dashboard is different from the filter you're running in your search. But without knowing what you're looking at on the dashboard, we can't really help you.
The rest of your question makes no sense. "Deleted the issues file" is nonsense - Jira does not store issues in files, so I have no idea what you think you're deleting. JIra doesn't ask you to delete issues. And you can't do anything with issues while Jira is locked.
My best guess is that you mean you tried to start Jira while it was already running or had been badly shut-down - this leaves a lock file in place, which you then have to delete to get it running again, after you have made 100% sure it is definitely not running. (If you did not check this and you've managed to start a second copy of Jira, you probably want to start checking for your backup tapes). If you have done a hard shutdown of Jira, then it's possible that you've damaged your index, which might explain the dashboard discrepancy in some cases. But I'm really not sure that's what you've actually done.
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