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As the question says, how to format a usb flash drive without formatting cos I don't want to lose data. I ran into an error that said file is too large for destination file system. And apparently it is to do with the file system of the USB.

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If you are unable to save a large file on a usb drive that has enough space, likely it is formated as a vfat filesystem. A better format that doesn't have this issue is exfat. The ntfs format is also an option, but not common on USB sticks and a poor choice if you are going to use it with linux, and at one time a poor choice for a USB in windows (but I think this is fixed now).

There are both Microsoft tools and third party tools that can convert the filesystem wintout destroying data (probably), but this is still extremely dangerous. If the drive fails during the conversion or the conversion gets interrupted for any reason, you will likely lose all data anyway. It would be better to make a backup of the data, format it, and then copy it back.

External drives are fragile and should be considered disposable anyway. You can lose them, drop them, or they could be stolen, and external drives have a finite lifetime even if you treat them well. Flash drives like usb drives have a limited number of write cycles. If the data is important, you should have another copy of the data somewhere else anyway.

user10489
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You can do this in windows as below:

Note drive letter for USB drive first.

Then Open command prompt as administrator,

At command prompt where it says system32/ run below command

CONVERT D: /FS:NTFS /NOSECURITY. Here D: is the drive letter for my USB stick.