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Checksums are valid upon opening the save file. Modifying things like changing the box might not be tracked as "edited", but the checksum will no longer match what is expected since the save was truly modified.1 point
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PKHeX is open source, read the source code or step through with a debugger if you must understand how it works. There's way too much to describe to waste time writing guides and wikis for every single file format and interaction. X/Y's format is described here, for both the raw save archive and main: https://projectpokemon.org/home/docs/gen-6/xy-save-structure-r82/1 point