1. $OldVariable contains characters special to the regexp engine -- prepend with \Q.
2. The random number may be repeated.
3. Once you've modified $code, @code isn't updated.
4. Your code doesn't deal with multiple arrays on a line.
5. The sigil for (scalar) array access is $, not @.
6. You aren't modifying any arrays that aren't indexed (for instance, your code leaves my @array untouched).
7. You're assuming there's no space between the array name and the index.
8. You're assuming the index consists of just a number, what if it's an expression, a variable, or has whitespace?
9. You're missing all the arrays containing capital letters, or that start with an underscore.

i'm aware of some of these problem thats where i need help :) all of the assumptions are people i will be the person who makes the files that are to be modified its for personal use.:) thanks

Reading your 'duplicate' post, I'm not quite sure what you are trying to achieve there. As to this post, the example below may be of interest. I think it should be suitable for either line-by-line or whole-file processing. 5.10+ needed due to use of  \K operator.

BTW: In addition to the problems with the code in this post pointed out by JavaFan, I would add that  int rand 9999 will only produce numbers in the range 0 .. 9998. I don't know if this was intended or not.

>perl -wMstrict -le
"my $s =
   'xx @ra[1] y @ara[23] z @ra[1] aa @ara[23] b @ra[1] @ara[23]';
 print qq{'$s'};
 ;;
 my %found;
 $s =~ s{ \@ ([a-z] [a-z\d_]* \[) \K (\d+) (?= \]) }
        { $found{$1 . $2} //= int rand 9999;       }xmsge;
 print qq{'$s'};
"
'xx @ra[1] y @ara[23] z @ra[1] aa @ara[23] b @ra[1] @ara[23]'
'xx @ra[2038] y @ara[6310] z @ra[2038] aa @ara[6310] b @ra[2038] @ara[
+6310]'
[download]

Update: Used  //= instead of  ||= in substitution replacement block code per Anonymonk's usage below.

Please let me to improve your code:

my $s = 'xx @ra[1] y @ara[23] z @ra[1] aa @ara[23] b @ra[1] @ara[23]';
print qq{'$s'\n};

my %found;
my %generated;
$s =~ s{ \@ ([a-z] [a-z\d_]* \[) \K (\d+) (?= \]) }
       {
            $found{"$1$2"} //=
        do {
            my $rand;
            do {$rand = int rand 9999} while exists $generated{$rand};
            $generated{$rand} = ();
            $rand;
            };
       }xmsge;

print qq{'$s'\n};
[download]

Fixed issues of producing something like this:

'xx @ra[1] y @ara[23] z @ra[1] aa @ara[23] b @ra[1] @ara[23]'
'xx @ra[1] y @ara[0] z @ra[1] aa @ara[2] b @ra[1] @ara[2]'
[download]

... producing something like this:
'xx @ra[1] y @ara[23] z @ra[1] aa @ara[23] b @ra[1] @ara[23]'
'xx @ra[1] y@ara[0] z @ra[1] aa@ara[2] b @ra[1] @ara[2]'


Good catch on the use of  //= versus  ||= in your code since the value of the generated random integer could, indeed, be zero leading to a redefinition on a subsequent encounter. I would quibble with
    $generated{$rand} = ();
however, since assigning the contents of an empty list to a scalar (i.e., undef) is very odd and likely to be confusing, it is much better, IMO, to assign 1 (or any true value) since that would slightly simplify the existence test to
    do { ... } while $generated{$rand};
(if, in fact, there is a requirement that the generated random integers be non-repeating).

ow.. cool.. could i also use a modified version of that to replace the array names to like a random string? i tried it myself but i cant replace with a string, only numbers...