From personal experience, the transfer will work just fine. Just be aware that all non-legit CIA's you've downloaded will be gone.Due to physical damage, I'm considering getting another New 3ds and doing a system transfer. I'm currently using latest Luma3ds. If I, before transferring, downgrade and get the target system's OTP and install A9Lhax, will the transfer work ok? (Using the 'switch sd card' option of course)
Edit: I also am considering sending it in to Nintendo to repair. Will they notice if I've uninstalled A9Lhax?