No idea how the chkdsk could have helped, since it didn't find any errors on the mass storage device, but it apparently did. All seems to work fine for now... Perhaps the freedownloader hack or something else messed the file system (?!)
(Before the chkdsk, whatever I put on the Kindle in mass storage was not visible from shell, but it was vice versa. To make it more confusing, files put on the mass storage and invisible in shell were visible again once reconnected as mass storage. The fat did not get updated?)
[OK, problem is back, again what i saved over the USB is invisible from Kindle. No idea what's happening
And again collections reverted to the state they were in two days ago. argh!]