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You have to put this map script with advance map in the map where the pokemon is
05 On map entering/On menu closing
#dynamic 0x8000000
#org @aftercatch
checkflag 0x8C1
if 0x1 call @hidesprite
end
#org @hidesprite
special2 LASTRESULT 0xB7
compare LASTRESULT 0x7
if 0x5 goto @return
hidesprite...
The colors in front sprite do not match the colrs in the shiny sprite, so you have to reorder the pallete of shiny sprite to match exactly the colors in the front sprite.