Any saves you have on the destination system will be gone once you do a system transfer. Aqua 3DS (Ambassador) > Transfer to MK7 XL (Keep Ambassador and MK7) > Transfer to AC XL (Keep Ambassador, MK7, AC I think it might be best for me to email Nintendo and figure out if this will work.
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It also supports loading ROMs from remote storage using network filesystems like NFS. Lakka supports loading ROMs from an external USB drive.