this is the reason of not updating stats. The filewalker is doing a similar command, so in your case it took more than 48h to complete. Seems you either use a BTRFS, or your disk is SMR.
this is only confirms the slowness of this disk.
You may try to re-create a database storage_usage.db, but backup it first. You likely will lose a usage history after re-create of this database.