if it works in classic mode,
it should be able to decrypt saves that are made on 4.5 and below.
For that you need Gateway to patch their launcher.
only for games that have nand saving (card2), such as pokemon x.
to transfer the save, can you savefiler (dev app) or save data transfer tool (3ds ware dumped)
besides that, no other games can transfer their saves.
In addition,
making an existing card 1 rom to card 2 will change the header,
and the save will be seen as corrupted, so won't be able to transfer too.
(I tried)