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Now, I have the flash drive with two partitions, on one of them a live distro,
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When you boot the system on the flash drive and as root run: fdisk -l do you see the second partition?
If you do, can you create a mount point for it and mount the partition and then copy anything to it?
I expect that if you can, you would have to go through this process each time you boot.
I can't think of any reason why you could not use something like GParted to delete or format those partitions. Have you tried creating a new partition table for the flash drive? If you do that, make sure you have the correct drive!
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even when formatting the drive on a Windows machine does not work. eventhough it says the drive has been formatted. (only the partition with the distro on it!)
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With a flash/pendrive seen as a 'removable device' in windows, windows only see the first partition which explains that result. With an actual usb hard drive you can create and use multiple partitions on windows. You might be able to use some third party software discussed at the windows 10 forums in the link below or change it so it does not show as removable.
https://www.tenforums.com/drivers-ha...ash-drive.html
A new partition table seems like the simplest solution if you just want to clean the drive.