Briefly, what's the easiest way to remove Ubuntu from a USB key? I'd usually just take it off with a Linux Live Creator batch file, but for whatever reason this particular live USB wasn't made with L.L.C.

Format the partitions(s) on the usb drive.

or if you want the lazy mans way to do it. hook it up to a windows computer and do a quick format unless you want to install ccleaner like I use and do 3 formats on the drive then use it.

Do not forget most USB drives are formatted for Fat32

Don't want to do that, as I have my C: drive backed up on it. (I tried making a system image on USB, but Win. insisted I didn't have the right kind.)

How did you put Ubuntu on the flash drive? Generally, software such as unetbootin/pendrivelinux will use a FAT32 partition for a Linux Live CD on a flash drive. Did you do a Live CD install? Did you just copy the Ubuntu iso file to the flash drive and boot it from Grub on your hard drive? Did you do a full install? I would think you would need an ntfs partition for a windows backup but I haven't used windows for years so don't really know.

I'm not sure, but I know it wasn't just copying the .iso file.

Do you know how many partitions you have on the usb?
Do you know what filesystem types on the partition(s)?

There's only one partition, format fat32.

I assume if whatever software was used displayed a message that all data will be overwritten that you would of cancelled the operation and therefore your backup is still intact. I also assume that you have examined the drive to see if your backup is still intact.

The disk creators that use a FAT32 I believe basically extracts and copy the files to the drive and then use syslinux to make it bootable. I have not heard of delete or restore feature for the flash drive. Just by examining the drive you should be able to find those directories that are part of the Ubuntu and delete them. If unsure you could extract the files from the ISO and compare them with the contents of the flash drive.

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There's only one partition which is both an Ubuntu live installation and a backup for your Windows system? That doesn't make a lot of sense...but either way can you find the directory where your Windows drive is backed up to and delete everything else?

Hit it with a hammer.