To my surprise it worked fine.

I'm surprised too. You should have gotten a 'Variable "@files" will not stay shared' warning.

Minimalistic example:

sub foo {
    my @files;

    sub bar {
        push @files, @_;
    };

    bar(@_);

    return @files;
}

print join ' ', foo(123, 456);       # prints '123 456'.
print join ' ', foo('abc', 'def');   # prints nothing.
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So why doesn't it print anything the second time? It's because &bar will have its own @files array but &foo will get a new array each time. So &foo and &bar will only share @files the first time &foo is run.

Another (expected) solution and its problems:

my @files;
sub foo {
    bar(@_);
}
sub bar {
    push @files, @_;
}

foo(123, 456);
print join ' ', @files; # '123 456'

foo('abc', 'def');
print join ' ', @files; # '123 456 abc def'
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We need to reset @files somewhere. OK. Let's add @files = () at the beginning of &foo.
There! Now it works... or not. It can't handle recursion. Let's modify &foo some more to make it a recursing subroutine:

sub foo {
    @files = ();
    bar(@_);
    shift;
    foo(@_) if @_;
}
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Now the output will be '456' and 'def' instead of '123 456 456' and 'abc def def' respectively. So we can't do the @files = () assigment in &foo. We need a wrapper. But what if the wrapper mysteriously gets recursive? Evil indeed...

My solution:
Keep it simple, keep it clean, keep it working.

The non-recursive solution to the original problem. (Of course rewritten as well, I'm just interested in showing the technique.)

sub foo {
    my @files;

    my $bar = sub {
        push @files, @_;
    };

    $bar->(@_);

    return @files;
}

print join ' ', foo(123, 456);       # '123 456'
print join ' ', foo('abc', 'def');   # 'abc def'
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Here the inner subroutine gets recompiled each time resulting in @files always being the same as the one &foo uses.

Making it resursive:

sub foo {
    my @files;

    my $bar = sub {
        push @files, @_;
    };
    
    $bar->(@_);

    shift;
    return @files, @_ ? foo(@_) : ();
}

print join ' ', foo(123, 456);       # '123 456 456'
print join ' ', foo('abc', 'def');   # 'abc def def'
[download]

Viola!

I hope no one got confused by my rewritings from the original problem.

Cheers.