If they got transferred when you did the system transfer then no, they shouldn't impact anything.
I'm not 100% sure about this, but I don't know how these files could impact anything,
since they're just NAND-Backups and payloads you can use once you've installed A9LH.
A9LH itself doesn't get transfered afaik, otherwise we could just system transfer a 3DS that was already hacked to a new one and that would be it.
Correct me if i'm wrong though, guys.