The Song of Time should save basic progress like your masks and other progress, various tokens, and remembering which cinematics or triggers you've seen before to skip them next time. (Tatl only nags you the first time you enter Woodfall to comment about the summoning pedestal, the motion blur part where Link gets sucked up into the moon in bird's eye view gets removed, etc.)
If this does not work correctly it could be a bad file Project64.rdb. The masks should be saved, but immediately after returning the evil to conealation under the mask of imprisonment the game should save right there in the same way.
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