Changing the file system from the run command is not reformatting and will not destroy the files.
Follow Monument's instructions and your files will be safe. Also click here
Just be aware that it is easy to convert to NTFS, you cannot convert back to fat32 without a format, though it may be possible with partition magic. This is worth bearing in mind if you think you may need to use the external hard drive on a standalone windows 98se/ME system.