OLD BUGGED CODE:
sub remove {
    my ($cpio, @filenames) = @_;
    $cpio->{list} or die "can't remove from nothing\n";
    my %filenames = map { $_ => 1 } @filenames;
    @{$cpio->{list}} = grep { !$filenames{$_} } @{$cpio->{list}};
}
[download]

WRONG NEW CODE
sub remove {
    my ($cpio, @filenames) = @_;
    $cpio->{list} or die "can't remove from nothing\n";

    foreach $item (@{$cpio->{list}}) {
        foreach $file (@filesnames) {
            if ($item->{name} eq $file){
                delete @{$cpio2->{list}->{$item}};
            }  
        }
    }
    return;
}
[download]

The only flaw of the old code is that it directly compares elements from @{ $cpio->{list} } against the filenames. That is wrong because the elements in @{ $cpio->{list} } are Archive::Cpio::File objects. Instead, it should compare the elements against the ->name property. Most likely (but untested) like so:

sub remove {
    my ($cpio, @filenames) = @_;
    $cpio->{list} or die "can't remove from nothing\n";

    # Create a lookup table of names to be removed
    my %filenames = map { $_ => 1 } @filenames;

    # This was the old, buggy code
    # @{$cpio->{list}} = grep { !$filenames{$_} } @{$cpio->{list}};

    # Remove the elements according to their name:
    @{$cpio->{list}} = grep { !$filenames{$_->name} } @{$cpio->{list}}
+;
}
[download]

This seems to work (the first output was correct)
Thank you!