>>906
flat使わなくてもいい

for(let i = 0; i< array.length; i++) {
for(let j = 0; j< array[i].length; j++) {
if(before.includes(array[i][j])) {
array[i][j] = after[before.indexOf(array[i][j])];
}
}
}

map使うなら
array2 = array.map(r => r.map(c => before.includes(c) ? after[before.indexOf(c)] : c));