The SetToSAV Modify Dex doesn't touch the dexnav counters (it could, maybe I'll just enable it to change 0->1 and that's it).
The Encryption Constant is the 'seed' which encrypts the Pokémon; for past gen pkm it should be equal to the PID, but it really doesn't matter (it's not checked by any legality check).
edit: Implemented 0->1 in latest commit. Won't be posting a new version until it's warranted, feel free to compile