Hello @DI2E SysAdmin,
It's safe. It would be a good idea to backup the current index: $JIRA_HOME/caches/indexes. Then cancel it and perform a full background index (scheduled downtime). In the worst case scenario you can always restore the backup index. Also you can manually rebuild the indexes by shutting JIRA down. Clearing the contents in $JIRA_HOME/caches/indexes. Upon starting JIRA again it will rebuild the indexes from scratch. If you continue to have issues please open a support ticket. We'd be more than happy help!
The re-index purposes is to only fix indexes problems with JIRA, if you were to stop it in the middle of the process it might for sure leave some wrong entry or unfinished updates but it won't cause your application to be unusable, although some feature that depends on the indexes, like searches and other reports might not work as expected.
You can always rebuild your indexes by the way.
I hope it helps!
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