Sometimes chicks are born with problems that can't be solved, internal issues. They're so tiny, it's hard to tell what exactly is wrong. But their little bodies just are not quite right. You clearly did your best for the little one and gave him a good life while he was here.
It's very sad, as he was a cutie. Sorry again for your loss.
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Yes--there is a hole in the skull where the brain protrudes from the skull cavity.
I thought the vault was caused by a hollow bubble in the skull. The brain is still protected by a thin layer of bone, but it can fall into the bubble, and in some cases out of the bubble... at least, that's what I thought it was. Either way, the APA Standard has an excellent drawing of a vaulted skull. It's pretty wacky looking.
Roopty, I'm so sorry! Sometimes they're just not meant to live. I just lost two the other day that simply failed the thrive. There's nothing you can do but keep them comfortable. At least he's in heaven now... and he probably wears a very spiffy 10 gallon hat up there (that just seems right for him, it would fit very well). Hugs, I'm sorry for your loss.
He was a cutie-pie, but as others have noted, sometimes there are internal things we just don't, or can't, know about. You gave him the best you could; beyond that, nature has to take its own course.