First pretend you never made emunand before, sysnand keys will be 1,emunand will be 2,when you made your backup,all games were linked to 1,and when you create emunand,it makes a copy from sysnand meaning emunand keys will be 1 too so when unlinking by formating sysnand,it's keys switch to like ugh...3...so the saves and games in your sd card are still linked with 1 and won't work with 3,3=/=1,but it still works with emunand since both of the keys are 1 and sysnand is 3 meaning that's now unlinked nand, problem if you create a new emunand, it will have the key 3 since it copy's sysnand, and your sd backup files is linked to key 1 since it was made before emunand and you formatted after...get what im trying to say, the sd files don't match with current emunand keys
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To backup your emunand system, backup emunand with a tool and copy the sd files linked with it