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I have a Drupal 7 site and the queue table has over 4K records. They are primarily for the "update_fetch_tasks" queue. Is the queue table by nature a temporary place holder?

I would like to clean it out and see if it fixes some issues that I am experiencing with the update module. I've done some digging on the queue module and from what I can tell is that proper usage is to claim the queue items and when you are done with them you should delete them. So it seems odd that a core module is leaving records in the queue.

Is there any harm in removing records from the queue?

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That table is used by the BatchQueue class; on the top of the page I linked there is the following note:

Stale items from failed batches are cleaned from the {queue} table on cron using the 'created' date.

For some reason, in your case they are not being deleted during cron tasks; probably cron tasks are not enabled in your site, and the setting that allows cron tasks to be executed through JavaScript is not selected.
In any case, once batch operations are completed (which means also when the updates have been completed), it is safe to delete those database rows.

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