That's basically what I've been doing, except I have been opening the data folder using Windows Exploder after closing Newsbin.. I delete the nb2 files, then restart Newsbin. At that point the Parts corresponding to the nb2s I've deleted show as partially downloaded. Before 6.4, they would be virgins. When I went back to 6.31 this is what happened...fresh parts ready to start downloading.
I'll bet you're deleting them from the DOWNLOAD folder. I'm suggesting you delete the ones in the DATA\temp\ folder.
By default, it only puts the entire NB2 in memory if you set some hidden options. If you haven't done that then, it's writing to the NB2 during download. It's easy enough to confirm this one way or the other. Do some downloads and see if the NB2 is being written to during download. Since it doesn't fail for me. I'd like to give you test versions to try different fixes for this. To try to get to the bottom of it. That fact you're running XP might be related to this and might explain why it's not happening to me. I've noticed that thread timing is different between XP and Win7.
I have a version here for example that writes every binary block out to disk during download. It's a bit slower but, it would be interesting to see if that works for you. The NB2's aren't used at all there.
So, if you're game, I'll contact you when I have another version to try so, we can get some testing in. What I suspect is happening is timing. On exit, my version is able to save off the updated data but, because the exit timing is different for XP or CPU speed or something like that, you don't get a complete partial save.