In Linux a file isn’t deleted until every pointer to the file is removed. So for an example if you have a log file which is currently being written to and has grown to 5GB in size and you delete it, although the file will not be listed in your directory anymore because that pointer was removed, you won’t free up the disk space because there is still an active process on your system which has a pointer to the file and is still writing to it.

This is why when you are deleting from active files you want to restart the service in question otherwise all of the pointers won’t be removed and the free space won’t be reclaimed.

So if you are doing any file level operations to open files you want to restart the service, or stop it before performing them.

Very likely if you get your active services, in this case MySQL, you should reclaim whatever free space you actually have available.