Benjamin, I am a bit confused by the fact that in previous comment you did:
# fdisk /dev/sdb1
where I would have expected
# fdisk /dev/sdb

That said, I have reproduced something similar on a 1GB USB2 key running Hardy 
up-to-date.
I had a fat partition on it.
I used sudo fdisk /dev/sdb
then d 1 to delete fat partition, then n to create a new Linux partition 
filling it all.
But on w command, I received an error 16, device busy, and a message indicating 
that it would use
the new partitions on reboot.

So I did reboot. And to my surprise, I was still able to see my files on the 
FAT partition!
Nautilus reporting disk as vfat type. Was even able to open a small text file 
(although my bigger .pdf does
not seems to wish to open).
But fdisk -l or fdisk /dev/sdb followed by p command both show linux partition:
[EMAIL PROTECTED]:~$ fdisk -l /dev/sdb

Disk /dev/sdb: 1031 MB, 1031798784 bytes
16 heads, 32 sectors/track, 3936 cylinders
Units = cylinders of 512 * 512 = 262144 bytes
Disk identifier: 0x04c504c4
   Device Boot      Start         End      Blocks   Id  System
/dev/sdb1               1        3936     1007600   83  Linux
[EMAIL PROTECTED]:~$ 

My hypothesis for now, is that when plugging the key, system automount on 
/media/disk my /dev/sdb.
And I did not unmount /media/disk before doing sudo fdisk /dev/sdb.
Probably the system should have WARN me of that as soon I did fdisk /dev/sdb, 
but it did not.
It did warned me on w command however, contrary to original bug reporter it 
seems.
Not clear to me what is supposed to happen while editing partitions on a 
mounted device.

-- 
fdisk doesn't write partition table
https://bugs.launchpad.net/bugs/58331
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