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I need to clarify few things about dealing with updates, as I got PM about it:
After you unpack the update using basenca command(with conjunction of plaintext command you used on the original first version of the game), you get full new updated and extracted game as a result.
First thing you need to do is to rename ID in the database file to be same as original game. Usually updates end with something like 800 in last digits, say if original game was ending with something like ...A000, updated one could be ...A800. This is because ID of the update is(correctly) that, however, when packing back to nsp game again, it need to be ID of the original game, not an update!
Above only apply to updates, not DLC as those are standalone(and you don't use plaintext or basenca commands on them).
Furthermore, updated games will likely contain more than just control, logo and program nca's. Specifically they may contain data nca - even multiple. When you go to those unpacked nca's that are data(as pointed in database file), there should be single file called fragment. These nca's are useless and have to be removed: delete whole extracted data nca folder and also remove it from database file.
You should pretty much end up with only program, control and logo nca's(in 99% cases), with ID of the original game.
If you want you can also copy logo section from original version to updated version(and increase section number from 2 to 3 in database file), as original hactool do not do it. But is not mandatory.
@Masquerade let me know if it works for you now. Write me here about it.
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