This is quite a confusing, but interesting question. The idea is to build a second structure @tree that is a restructured version of @arr. @arr is assumed to be left as is?

The problem is that you are working with references to arrays, your are not copying the underlying arrays when you build @tree. So your line splice @{tree} ... is really inserting parts of @arr into the new variable and operate on them. If you replace this line by creating a copy of @$subNg and insert it into tree you should be fine (hopefully).

As a minor comment: I prefer to use Dumper \@arr as this creates a single structure and is more readable IMHO.

Proposed changes to leave @arr untouched:

    $tree[0] = $arr[0];
    my @copy = @{$arr[1]};
    $tree[1] = \@copy;

   ...

   
    my ($index) = grep { $tree->[$_] eq $treeElement } 0..scalar(@$tre
+e)-1;
    my @copy = @$subNg;
    splice @{$tree}, $index + 1, 0, \@copy;
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Whether or not this modified code creates the desired @tree I do not know.