The way I'd approach that would be to first make your code use the '-in' hash element as a hash array, rather than a fixed-format string. Next, I'd do the same with the '-like' element (I'm assuming it's existence from your question). Then, to use it, I'd split the string on the delimiter (|) to make a list and put each item on the appropriate list. Something like this (untested):

my @vals = split /\|/, $DocumentReference;
for my $V (@vals) {
    if ($V =~ /\*/) {
        $V=~s/\*/%/;
        push @{$where{DocumentRef}{'-like'}}, $V;
    }
    else {
        push @{$where{DocumentRef}{'-in'}}, $V;
    }
}
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Then, when it comes time to use it, you can create your IN clause like:

$SQL .= ' IN (' . join(", ", @{$where{DocumentRef}{'-in'}}), ') ';
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and your LIKE clauses something like this:

$SQL .= join(' OR ', map { "LIKE $_ " } @{$where{DocumentRef}{'-like'}
+});
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Note: You'll still need to ensure that the values are all quoted properly, and that you have the proper conjunctions between all your clauses, error handling, etc. etc.

...roboticus

Update: Moved last paragraph (it was accidentally in code tags...)

I am *not* sure this is right but might be worth playing with-

use strict;
use warnings;
use YAML;
use SQL::Abstract;

my $original = 'A*|B|C*|D|Z';

my @refs = split /\|/, $original;

my ( %like, %in );
for my $ref ( @refs )
{
    $ref =~ s/\*\z/%/;
    $ref =~ /%\z/ ?
        $like{$ref}++
        :
        $in{$ref}++;
}

# See what we've got so far-
print Dump \(%like, %in);

my $sqla = SQL::Abstract->new();

my @doc_like;
push @doc_like, doc => { -like => $_ } for keys %like;

my ( $stmt, @bind ) = $sqla
    ->where({
             -or => [
                     doc => { -in => [ keys %in ] },
                     @doc_like
                    ]
            });
print $stmt, $/;
print join(",", @bind), $/;
#
---
A%: 1
C%: 1
---
B: 1
D: 1
Z: 1
 WHERE ( ( doc IN ( ?, ?, ? ) OR doc LIKE ? OR doc LIKE ? ) )
Z,D,B,C%,A%
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