Aww, gee, you made me add one whole line to my program to handle your update, sigh :(

#!/usr/bin/perl

use strict; # https://perlmonks.org/?node_id=11107038
use warnings;

my @lines = <DATA>;
@lines = map /[^=:\s]*,[^=:\s]*/ ? map "$`$_$'", split /,/, $& : $_, @
+lines
  while "@lines" =~ /,/;
my %hash = split ' ', "@lines";
$_ = { split /[=|]/ } for values %hash;
use Data::Dump 'dd'; dd \%hash;

__DATA__
Prefix1=A,B:c,d value1=5
Prefix2=A:b,c:1,2 value2=6
Prefix4=A:*:1,2 value4a=10|value4b=20
Prefix5,Prefix6=A:*:1,7 value5=10
[download]

Outputs:

{
  "Prefix1=A:c"   => { value1 => 5 },
  "Prefix1=A:d"   => { value1 => 5 },
  "Prefix1=B:c"   => { value1 => 5 },
  "Prefix1=B:d"   => { value1 => 5 },
  "Prefix2=A:b:1" => { value2 => 6 },
  "Prefix2=A:b:2" => { value2 => 6 },
  "Prefix2=A:c:1" => { value2 => 6 },
  "Prefix2=A:c:2" => { value2 => 6 },
  "Prefix4=A:*:1" => { value4a => 10, value4b => 20 },
  "Prefix4=A:*:2" => { value4a => 10, value4b => 20 },
  "Prefix5=A:*:1" => { value5 => 10 },
  "Prefix5=A:*:7" => { value5 => 10 },
  "Prefix6=A:*:1" => { value5 => 10 },
  "Prefix6=A:*:7" => { value5 => 10 },
}
[download]

I tweaked your original tests to comply with your new specs. Is that valid? If not, you owe us a new test case.