The following code clearly shows what is going on. When you call foo for the first time, @a was shared by bar. Second time when you enter foo, bar does not share the new @a, instead it retains the old one.

use strict;
use warnings;

use Data::Dumper;

foo(1);
bar();
foo(2);
bar();

sub foo {
    my @a;
    push @a, shift;
    print \@a;
    print Dumper(\@a);
    sub bar {
        print \@a;
        print Dumper(\@a);
    }
}
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Here is the output:

Variable "@a" will not stay shared at c.pl line 17.
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ARRAY(0x1890e78)$VAR1 = [
          1
        ];
ARRAY(0x1890e78)$VAR1 = [
          1
        ];
ARRAY(0x18c2194)$VAR1 = [
          2
        ];
ARRAY(0x1890e78)$VAR1 = [
          1
        ];
[download]

Make @a_files a property of the class, and define those two methods at the same level. This shall resolve your problem, and the code is much clearer.