Last time I tried to use luckybackup, it deleted files on the source location, and it didn't even back up half the data. It backed up alot of folders but I don't think it actually recursed. I need to do a lot of data migration this weekend, so I think using rsync through luckbackup is the best option. I am just worried about deleting the source data as I want to do that manually AFTER verifying the data has been transfered properly. I tried looking through the manual but it mentions nothing about deleting data from the source. I am guessing I used some bad combination of commands. In this case luckybackup reports the rsync cli is:

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rsync -h --progress --stats -r -tgo -p -l -D --update --exclude=**/*tmp*/ --exclude=**/*cache*/ --exclude=**/*Cache*/ --exclude=**~ --exclude=/mnt/*/** --exclude=/media/*/** --exclude=**/lost+found*/ --exclude=/var/** --exclude=/proc/** --exclude=/dev/** --exclude=/sys/** --exclude=**/*Trash*/ --exclude=**/*trash*/ /media/WD3 /media/WD3TB/

That looks okay - although be careful as a variety of files/folders will be skipped if they match certain naming conventions.
You may want to try something a little more basic if you want to retain everything.

I am assuming you are copying from /media/WD3 to /media/WD3TB - and don't want to use any sub-folders.

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rsync -av --progress  /media/WD3 /media/WD3TB

Thanks for the tips bcooksley, However, that may not have been the same options used in the bad experience. I posted because nothing in the gui screams at me(figuratively speaking, I dont mean a nasty pop up or warning text - although that didn't happen either) that it is going to delete source files if I check mark an option.

Just to be 100% safe, you may wish to mount the source disk/volume as read-only so the files cannot be changed.
(Alternately, depending on the file system in use, run the rsync command under another user which has no permission on the source device other than read access).

Will read only access work for my OS drive? My boot drive is the only one I back up.

Unless you are using a Live CD - probably not. I was working off the assumption that /media/WD3 was an external disk, and therefore should be detachable - and mountable as read-only if necessary.

bcooksley wrote:Unless you are using a Live CD - probably not. I was working off the assumption that /media/WD3 was an external disk, and therefore should be detachable - and mountable as read-only if necessary.

Ah I see where the confusion lies. In this case, WD3 is an internal. I do not use externals, well I do use 2 but they are always attached to other devices at all times. This is also a one off case. I have 2 HDDs dieing on me at the same time. I bought a 3TB to replace one/possibly both. Before useing it as a replacement drive, I used it to back up my prospering sata 3 drive so I could convert ntfs to ext4. I did that but regret it as I am seeing a nearly 50%(perceived) drop in performance when extracting rar files or transferring media to my NAS.

Now, the real deal! I do not back up my data drives. I would hate to loose them, but everything on there can be lost if it came down to it. Technically I could say the same of my boot drive to. In this case it is more the inconvenience of doing a reinstall from scratch. However my boot drive is the one and only drive I perform back ups of.

Okay, in this case I would suggest using the "--dry-run" option to rsync to see what it would do before executing it. If backing up the operating system, permissions and ownership are ultra critical, so you absolutely must rsync to a linux native file system such as ext4.
You will want to ensure that /proc, /sys, /dev and /tmp are excluded from the backup of the boot/operating system disk using the --exclude options.