This is due to the fact that, some user processes keeps the deleted files open. "du" doesn't show that since the file (if it is removed), or the file contents (if it is cleared) is not there in the current working directory.
"df" will continue to display the previous disk space, until the space is de-allocated. To de-allocate this space either the file descriptor of the file should close or the process should exit.
Therefore you can try restarting the daemons used by these files or reboot the server.
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