This appears to be by design. I have a user who used unique permissions on a subsite and then used unique permissions on a list in the subsite. They then decided to have the subsite inherit permissions from the Parent and whoala, the list didn't retain the unique permissions.
So, what if the Securable Objects (a List) has unique permissions AND the subsite has unique permissions and the owner decides to have the subsite inherit from the parent? It appears the (list) in the subsite also inherits from the parent (meaning, its unique permissions are no retained). Is this by design?