Whew! It's possible the mum gave her new BF (boyfriend) permission to "discipline" GD, and, unfortunately, his method of "discipline" is spanking/hitting. And the mum may have felt guilty/embarrassed when she found out your DS (dear son) found out about it, so she told him it was a lie. Just speculation on my part, I know. But if it's true, she threw GD - a child - under the bus to save her own skin - Ugh!
"I then heard my granddaughter parrot that by saying I don't know what's wrong with my brain."
This^ sounds like they're also telling GD "it's all in her head," as they told DS. (Again just speculation on my part, I admit). Whether GD really is lying or her mum is gaslighting her, making her think there's something "wrong" w/ her "brain" is clearly abusive, even if mum doesn't realize it.
I'm so sorry about this and wish I had a foolproof solution. All I can do is echo the advice to let her know you believe her and, at least, discuss the situation w/ NSPCC as MOnica recommends above. I hope this is all straightened out soon.