open(FILE, $file) or die $!;
@lines = <FILE>;
close FILE;

for ($i = 0; $i <= $#lines; $i++) {
  if ($lines[$i] =~ /<% INCLUDE file(\d+)\.txt %>/) {
    $num = $1;
    # UPDATE:
    # ok, the next line (original) is wrong, see replies
    # $num = $num == 1 ? 1 : 2;
    # We have to write it this way:
    $num = $num == 1 ? 2 : 1;
    $lines[$i] =~ s/<% INCLUDE file(\d+)\.txt %>/<% INCLUDE file$num\.txt %>/;
  } else {
    next;
}

open(FILE, ">$file") or die $!;
print FILE @lines;
close FILE;