I'm not entirely sure, although i will contribute by sayinf that 3DSLink is a clone of Gateway 3DS (probably an earlier version prior to the bricking fiasco) But Gateway has had many updates since then, I'm unsure if the saving methods have changed. Your issue kind of proves that.
You didn't format your internal SD card whilst changing from 3DSLink to GW? You've made sure the files are on the internal SD card and not the Gateway micro SD yeah?