Most likely your problem is that you try to reread using DIR without reopening it. However there are a number of things that will help to tidy your code up. Consider (untested):

#!/usr/local/bin/perl
use strict;
use warnings;
use Archive::Zip qw( :ERROR_CODES );

my @testFiles     = listFiles ('C:\Perl\test');

# while loop to try every min for 3 mins if any the file counts a & b 
+don't match
my $retries = 0;
while ($retries++ < 3) {
    my @compressFiles = listFiles ('C:\Perl\compress');

    if (@testFiles == @compressFiles) {
        compress (\@compressFiles);
        unlink @compressFiles;    #delete compressed files
        unlink @testFiles;        #delete test files
        last;
    }

    print "Count Compare Failed!\n";
    sleep 60;
}


sub listFiles {
    my ($dirName) = @_;

    chdir ($dirName) or die "Can't chdir to $dirName: $!";
    opendir my ($scan), $dirName or die "Couldn't opendir $dirName: $!
+\n";

    return grep {$_ ne '.' && $_ ne '..'} readdir $scan;
}


sub compress {
    my @add_array = @{$_[0]};
    my $obj = Archive::Zip->new ();    # new instance
    $obj->addFile ($_) foreach @add_array;    # add files

    if ($obj->writeToFileNamed ('testing.zip') != AZ_OK) {    # write 
+to disk
        print "Error in archive creation!";
    } else {
        print "Archive created successfully!";
    }

}
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Note in particular that an array in scalar context provides the number of elements in the array so the test file count is simply @testFiles for example.

If you find yourself repeating more than a couple of lines of code consider using a sub instead. In this case listFiles not only makes the code more compact, but clears the flow up so it's easier to see where the error was.

Note that this code does not compare files, but only the number of file and directory entries in the subject folders. In particular, if files change names, but the number of files don't this code (probably) will not do what you want!