You cannot transfer any unsigned/illegally signed/whatever you want to call pirated cias to another ds through system transfer. The only games that will pass are legit cias (the ones that were dumped from consoles with pre-installed games). Save files of any games you have obtained somehow can be backed up and restored through save managers in homebrew or wherever else you have save managers.
Legit CIA"s also won"t transfer unless you have bought them later in the eShop or in Nintendo web site with your NNID, the tickets from titles are transfered from Nintendo servers and not the console tickets so you only keep content you bought and still own (for example if Nintendo unliked a bought game but you can still download it because you still have the ticket for it, but efectively it isn"t anymore in your Purchase History it also won"t be transfered as it isn"t linked to your account). Of course you can still use the other SD Card but the games aren"t going to be usable becuase there isn"t a valid ticket in the console, so the games only will appear in Management Data with a cross in them because them aren"t usable.
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