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fsck (file system check) type man fsck
It will remove stale inodes, etc. you should be right after that.
FSCK(8) MAINTENANCE COMMANDS FSCK(8)
fsck - check and repair a Linux file system
fsck [-sAVRTMNP] [-C [fd]] [-t fstype] [filesys...] [--] [fs-specific-options]
fsck is used to check and optionally repair one or more Linux file systems. filesys can be a
device name (e.g. /dev/hdc1, /dev/sdb2), a mount point (e.g. /, /usr, /home), or an ext2
label or UUID specifier (e.g. UUID=8868abf6-88c5-4a83-98b8-bfc24057f7bd or LABEL=root). Nor‐
mally, the fsck program will try to handle filesystems on different physical disk drives in
parallel to reduce the total amount of time needed to check all of the filesystems.
If no filesystems are specified on the command line, and the -A option is not specified, fsck
will default to checking filesystems in /etc/fstab serially. This is equivalent to the -As