Is anything lost with a system transfer (PC-based) ?

vertebrae4498

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I am aware that there needs to be a separate operation for CFW applications using faketik for them to transfer over properly, but I know how to do that (using the wiki hacks guide page on this).

My searches online don't seem to indicate that anything else is lost when doing a system transfer, but is that definitely the case? Is there anything on the target system after the transfer that would be different than it was before the transfer apart from the obvious (like being a different 3DS model for example), even anything very minor? Any pitfalls I should of? I will do a NAND backup, but just wanted to make sure everything was safe before I proceeded
 

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