Linux – EXT4-fs error (device loop0): ext4_lookup: deleted inode referenced:

Looks like your disk needs a cleanup. You should force a fsck on it to clean up all these errors before it craps out on you totally.

There are a lot of switches available with fsck, but to get you started you can do one of the following:

This will check all mounts in your /etc/fstab file:

fsck -A

This will check the particular disk that is throwing those warnings:

fsck -t ext3 /dev/<device name>

You should be aware that an fsck can take a LONG time so this is not something you want to do in the middle of the day on a production server.

The XFS filesystem would be a more supportable (long-term) solution for what you're trying to do now. Large file-count directories are not a problem for XFS. Of course, fixing this at the application level would also be helpful...