It appears videos that don't earn revenue get deleted after so many days. I've had the same issue. I read an article last night where the developer states that videos that end up with zero dollars and zero cents don't get permanently stored and this is the cause of this problem: https://steemit.com/dtube/@heimindanger/dtube-0-2-faster-to-serve-videos-stronger-to-resist-censorship

The only videos I have that wont play anymore are the ones that didn't earn any revenue, so the developer is serious. That's just the way the platform was designed, and likely was done this way to keep from indexing junk or spam videos. Or as the developer seems to assert, videos that many find controversial and might not want on the DTube platform. 

I dont do anything controversial, just gaming videos. But the lack of getting paying upvotes killed several of my videos anyway. 

The platform isn't perfect either. One of my videos never played at all! It simply did not work. In that particular case I think its exactly what you stated, the node that held the video is gone.