As far as I know, there is no such tool available under Linux.
The only solution is to back up the data, format the partition with the new FS and then, restore from the backup.
Also, if you really don’t want to access that file system from another Windo$ machine (I have the feeling that you don’t like Windo$ ), then, I suggest you create a better Linux FS than the proprietary M$ FS.
And I would add that whatever road you decide to take, make a backup of the info on the hard drive first because you never know when something might happen.