it is not always a good idea to re-index production especially if you have loads of items (workflows, custom fields, plugins, tickets, projects...) and you do re-index to often. Well obviously you won't be able to stop it right now and it is no usually a good idea. But if it keeps going that way. I would stop jira, restart it, do the foreground indexating : https://confluence.atlassian.com/jirakb/reindex-jira-server-using-rest-api-via-curl-command-663617587.html
Also for this time make sure you do it in a time range large enough after working hours (weekends for instance).
One good practice, once you know how long the foreground indexing takes is to use CRON to automate the foreground indexing every weekend. This way you make sure your instance is always on top of its performances.
If you have performances issues, you should check also the memory, the CPU, the Disk size and speed...
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