If you have an ITSI instance, you probably have a support contract, please open a support case for deeper troubleshooting.
From the description of the question, here are some pointers.
the itsi_refresh_queue is a kvstore collection used to store the changes to apply to ITSI, it can fill up when you have service-templates change to propagate, entity import, shared-bases-searches update, threshold updates...
If you had a recent mass change or an upgrade, this could be the reason.
after a refresh task has being applied, an object will be removed from the collection.
However the kvstore is a file storage, when a collection is growing, it will add new chunks of files on disk to reserve disk space.
But when the objects are removed from the collection, the files on disk will not be removed ( instead, the reserved slots we be reused later). So the disk space will not be recovered.
This may be what happened to you, a large collection grew big and did not shrink when the objects were removed.
To check :
You can check the collection size on the ITSI healthcheck dashboard, look at the "KV Store Collections" and "Number of Objects" versus "Collection Size (MB)"
or directly the disk on $SPLUNK_HOME/var/lib/splunk/kvstore/mongo/s_SA-ITO* files, but it may be hard to find which one is mapped to which collection.
If you have an empty collection (zero objects), but a large collection on disk, a one time workaround could be to clear the kvstore collection
./splunk clean kvstore -app SA-ITOA -collection itsi_refresh_queue
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