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Regional Pokédex scripts will overwrite anything you've seen (and owned if you use the "owned" version) which may cause you to lose registration of anything not in your game's regional Pokédex
These scripts will fill your dex enough to unlock access to the following rewards:
DP, PtSinnoh seen: regional dex diploma, National dex upgrade
XY, ORASNational owned: national dex diploma, Shiny Charm
SM, USUMAlola owned: Shiny Charm
National versions will also unlock access to all corresponding regional rewards
owned versions will also unlock access to all corresponding seen rewards
Complete versions will unlock all the same rewards as the National owned versions
Only the Complete versions will fill in Mythicals (Mew, Celebi, Jirachi, etc.)
Only the Complete (illegal) versions will unlock all forms and shiny sprites, including unreleased ones
Mass Inject
All mass injection scripts target the first slot of Box 1 to start injecting the collection. If you're worried about losing some of your Pokémon, make sure to clear out enough of your in-game boxes to make room
Living Dex
Gen 5: 22 boxes
Gen 6: 25 boxes
Gen 7: 27 boxes
Colosseum: 2 boxes
XD: 3 boxes
everything else: 1 box
Not all Pokémon in the mass injection scripts may be legal
Only the "Living Dex" scripts update your dex. If you want the contents of a mass inject script to be registered but don't want the full Fill Dex, do one of the following:
deposit the unregistered Pokémon in the Day Care then withdraw them
take them into a wild battle (reported to work but not confirmed)
rBreedingDitto: the Ditto in these scripts were obtained from this list on /r/BreedingDittos. They are subject to all the conditions and limits set by /r/BreedingDittos (so don't try passing them off as legal on /r/pokemontrades)
Fixes
All bag pouch scripts now have legal (available through normal gameplay and events) and illegal (all items) versions where applicable