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}}
+;
}
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