gparted check option messes up FAT formated drives

The check option in the version of gparted that is in the Ubuntu 16.04 LTS repositories has a known bug. When you run it on a USB drive formatted to either FAT or FAT32 it changes the drive. While the drive will still work on a Linux Machine it will not work on a Windows machine or another device that you might want to plug it into. I contacted the gparted folks on the gparted forums. Here is what the Developer said:

Ubuntu 16.04 does not contain the upstream patch according to the Ubuntu Parted Changelog.

Perhaps you could report the issue upstream to Ubuntu or even Debian?

As mentioned before, you can hexedit and change the first three bytes to be "eb 58 90" so that Windows will recognize the FAT16/32 file system.

The problem is not in the GParted source code. The problem is in the parted 3.2 source code. Hence it does not matter which version of GParted you use. The key thing is to use a patched version of parted when resizing FAT file systems. This patched version is included on recent GParted Live images.

To fix recognition of the FAT file system after the problem has occurred, the file system needs the first three bytes to be set to "eb 58 90".

Source link: http://gparted-forum.surf4.info/viewtopic.php?pid=34407#p34407