how does it not work? does it error? behave badly?

Be sure to always use strict;

$column[1] eq IN needs quotes around IN (strict would catch this). But otherwise, looks pretty close

open(FILE, ">$ffdb");
foreach my $line (@ffdbdata) {
  chomp $line;   # <--- use this instead of  s/\n//g
  my @column=split /\|/, $line;   # <-- no need for quotes: "$line"
  if( $column[0] == $ID ){
    $column[1] = $column[1] eq 'IN' ? 'OUT' : 'IN';   # flip the value
  }
  print FILE join("|", @column), "\n";   # do one write statement
}
close FILE;
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