When Neal explains things the problem partially makes sense and yet is still confusing. If only because she'd really thought Henry had moved past that dislike of Baelfire stage of his. She doesn't know why a change in location would prompt a relapse.
"It's not that you're his father that's the issue. It's that you're Baelfire." Thus Gold's biological son. Which is still a bit awkward to think about at times. "Have you done anything that might suggest you're going to take his father away from him since you've gotten here?" That had been Henry's original reason for treating the man like shit before. Perhaps Neal had done something that Henry had taken the wrong way and thus revived that old fear and grudge.
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"It's not that you're his father that's the issue. It's that you're Baelfire." Thus Gold's biological son. Which is still a bit awkward to think about at times. "Have you done anything that might suggest you're going to take his father away from him since you've gotten here?" That had been Henry's original reason for treating the man like shit before. Perhaps Neal had done something that Henry had taken the wrong way and thus revived that old fear and grudge.