Videos disappears from iPod!

I'm using a third party encoder for videos for my iPod, and I'm able to view them perfectly, the problem is:
When I update my videos (add/change/remove) on the iPod the ones that I didn't even touch will disappear and I'm only able to see them on iTunes, the new/edited ones show up correctly.
What am I doing wrong? Or what is the problem?
Thank you very much in advance.

I've got the same thing. I've posted a message, but no one answered. After sometime, I've found a work-around solution. I've got a 3rd part software (Ipod2PC) to move the movies or/and Mp3's to the hard disk.
What I did is, I moved the movies back to my hard disk (Oh yah, you need free space!) then, delete the ones on my Ipod using iTunes, then upload them back to the Ipod!
I am like you, waiting for someone to give me a final easy solution for this problem.

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