Sorry, typo. I meant your New 2DS. Install CFW on it, then make the transfer.
Yep, the hack doesn't get "transferred", so it stays on the N3DS, but you have to install it to the N2DS for your non-legit games to work after the transfer.
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You can follow this guide to install CFW in your N2DS, while restoring your NAND to your N3DS after the transfer:
https://3ds.guide/installing-boot9strap-(dsiware).html
If you have a NTRBoot enabled DS cart, just install CFW using NTRBoot before the transfer, and skip the DSi legit eShop title buy.
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Your saves and everything will be usable in your N2DS after the transfer.
Games installed from freeshop or from CIA files won't appear in the Home Menu. This is easy to solve for games on the eShop. Just install their tickets using a homebrew app like CIAngel, TIKShop/TIKDevil/TIKSweep, and they'll re-appear, all with your game saves working.
Sadly, this won't work for titles not in the eShop. Like VC injects, or homebrew apps.