Well... dang. I also discovered this bug, making the final level impossible to access, at first I thought I hadn't done it right, until I noticed that a couple of the stars just weren't being remembered on restart. One one hand, I'm glad it's known about and will presumably be fixed at some point; on the other hand, I sort of assumed if I tried the beta and everything was working flawlessly right up until the last level, it would continue to work there, too. My mistake, I suppose.

I do have to say, other than the lack of working access to the final level, it is an extremely gorgeous, and generally bug-free game in HD. Though I also have to say, the sound that plays when you enter or exit the final zone from the main zone select page is kind of jarring, too - but I probably wouldn't have noticed that if I hadn't just entered and exited it a bunch of times in a row, trying to figure out what was going wrong.

Anyway, I'm also amused by how easy it was to locate the save file responsible for keeping track of what I'd completed, so I just copied that to the not-HD's save file, and all good (other than I don't get to play it in HD. But oh well.) That also means I can tell you, it's definitely a problem with loading save file, not with saving it: my save file correctly says I've found all the stars.

edit: I just realized, given that they do share the same save file schema, obvious workaround, just copy the save file, use regular NightSky to get past the two levels that don't work in HD, then copy the save file back to HD, and you win!