That's a funny approach, but is not very efficient, every time you're assigning to $line[$i] it rewrites all the file starting from the record $i.

Update: More efficient would be to use File::Slurp:

use strict;
use warnings;

use File::Slurp qw(edit_file_lines);

sub fix {
    my @fields = split / +/;
    $fields[1] = sprintf "%-50s", $fields[1];
    $_ = join ' ', @fields;
}

edit_file_lines \&fix, $file_name;
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The problem is that it doesn't preserve the width of the other fields