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I figured out the solution by myself. The problem is caused by the unhealthy status of Ceph, so nova compute service cannot access the instance data, marking deleted instances as still existing.

Some Ceph OSD's were down because of disk failure and network issue, causing several PG's (placement groups) unclean and inactive. So I manually deleted these failed OSD's and marked them as lost, restarted online OSD's, abandoning lost data, and fixed all the failed PG's. After doing all of these, the compute nodes are brought back to 'up' state, and instances can be deleted properly.