Changing upper to ascii and using your string, I get:

$ perl -Mstrict -Mwarnings -E '
my $x = q{çe quil Y a Yå};
$x =~ s/([[:^ascii:]])/unpack q{H2}, $1/eg;
say $x;
'
c383c2a7e quil Y a Yc383c2a5
[download]

Check that you didn't make a typo when entering your code. If you are still having problems, please post your code - as it is, I can't reproduce your problem.

To wrap the codes in < and >, or any other characters, you can just concatenate the characters at the beginning and end of the hex code:

$ perl -Mstrict -Mwarnings -E '
my $x = q{çe quil Y a Yå};
$x =~ s/([[:^ascii:]])/q{<} . unpack(q{H2}, $1) . q{>}/eg;
say $x;
'
<c3><83><c2><a7>e quil Y a Y<c3><83><c2><a5>
[download]

I double checked the code and haven't found any typo:

#!/usr/bin/perl

$file = @ARGV[0];
$out_file = $file.".out";
my $count = 0;

print "Processing file: $file\n";
print "Output file: $out_file\n";

open FILE, "$file" or die "cannot open $file file";
open OUT, ">>$out_file" or die "cannot create $out_file file";

#go through the file rows
while (<FILE>) {
        chomp;
        # if row contain non-ASCII symbols - it is counted
        if ($_ =~ /[[:^ascii:]]/) {

                print "String before modification:\n $_ \n";

                s/[[:^ascii:]]/q{<} . unpack(q{H2}, $1) . q{>}/eg;

                print "String after modification:\n $_ \n";
                print OUT "$_\n";
                $count++ ; }
        else {
                print OUT "$_\n";
        }
}

print "there are $count possibly corrupted rows\n";

close FILE;
close OUT;
[download]

the contents of processed file:

0,1,,,1,~=_<>}[]||$? £??§^`??¿  ?. Qu est  çe quil Y a Yå,0,20120
+306101731
0,1,,,1,Teá,0,20120314104403
0,1,,,1,Q<8a>rUì ,0,20120306103345
1,1,,,3,,0,20120331152610
1,1,,,3,,0,20120331152612
[download]

Thanks, Ken! I found the typo - forgot to put the search expression in brackets ([...]). Let me say that I am sorry for my impatience. :)