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I'm using Transmission 2.82 on Xubuntu 14.04, and I noticed that after I deleted the downloaded file permanently from files manager, the job in Transmission was still active and kept seeding, and there was no change in free disk space, so I tried ls -l /proc/[pid]/fd and I got this:

lr-x------ 1 name name 64 May 4 20:39 81 -> /home/downloads/ubuntu-16.04-server-i386.iso (deleted)

then I redownloaded the file and deleted it with rm without deleting the job and the disk space was freed and ls -l /proc/[pid]/fd gived no entry related to the file and the job was seeding at 0kb/s.

but to see if it was rm that made the difference, I then tried three times delete the downloaded file with rm while the job was seeding, and each times I received the same result, the jobs were active and seeding, no change in free disk space, and ls -l /proc/[pid]/fd yielded something like:

lr-x------ 1 name name 64 May 4 20:39 26 -> /home/downloads/ubuntu-16.04-server-i386.iso (deleted)

and ls ubuntu-16.04-server-i386.iso gived:

ls: cannot access ubuntu-16.04-server-i386.iso: No such file or directory

I also tried du -s and df /home in the download folder with another job respectively when:

Job running, file undeleted:
$ du -sh
11G
$ df -h /home
Filesystem Size Used Avail Use% Mounted on
/dev/sda1 58G 54G 1.2G 98% /

Job running, file deleted(with rm) (and Transmission keeps seeding after deletion):
$ du -sh
9.9G
$ df -h /home
Filesystem Size Used Avail Use% Mounted on
/dev/sda1 58G 54G 1.2G 98% /

Job deleted, file deleted(in previous step):
$ du -sh
9.9G
$ df -h /home
Filesystem Size Used Avail Use% Mounted on
/dev/sda1 58G 54G 1.5G 98% /

So, what happened to the downloaded file? After I rm it, how Transmission is still seeding the job? Is it possible to restore the file? Since du and df give different outputs, is the file relocated to some other place?

If a program has a file open when you delete it, the kernel only marks it as deleted, but doesn't free the disc space, to avoid breaking the program (it's can't know if the file is important to the function of the program). When the program closes the file the disc space is freed. When that happens you will see the "(deleted)" when you look at /proc/<pid>/fd for the process that has the file open.

So this is the kernel being helpful in not removing a file that transmission uses.

If you don't want to share a file using transmission you should remove it from transmission, as far as I remember transmission even has an option for deleting the files as part of stopping to share it.

You can actually restore the file by copying it from /proc/<pid>/fd/ since it is a link to the file (just one that only exists as long as the process has it open).

root@mypc:~# pgrep transmission

1470

root@mypc:~# cd /proc/1470/fd

root@mypc:/proc/1470/fd# ls -l | grep deleted

lr-x------ 1 user user 64 Dec  8 02:55 56 -> /mnt/download/my.file (deleted)

root@mypc:/proc/1470/fd# cp 56 /mnt/download/myrestored.file

I suspect transmission saves the file to a location unknown to you when downloading. After it is finished it creates a hardlink to that same file in your download folder, but still keeps the hardlink in it's own directory(probably ~/.transmission or something like that).

You can find all hardlinks to the finished download as explained in How to find all hard links to a given file? or use this:
Go to ~/Downloads execute ls -i and remember the inode-number for your file. Then you can find the other file by executing find . -inum NUM in your home folder.