There's a trick that helps with deep structures:

my $flow_id = $data{partners}{$part_id}{flow};
for my $wfref (@{$data{flows}{$flow_id}}) {
    #...
}
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While not necessary here, you can always break things down further:

my $partner = $data{partners};
my $flow_id = $partner->{$part_id}{flow};
my $flows_ref = $data{flows}{$flow_id}};
for my $wfref (@$flows_ref) {
    #...
}
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or

my $flow_id = $data{partners}{$part_id}{flow};
my $flows_ref = $data{flows}{$flow_id}};
for my $wfref (@$flows_ref) {
    #...
}
[download]

But in this case, I don't see why flows and partners are in the same structure

Change %{$data{flows   }} to just %flows.
Change %{$data{partners}} to just %partners.
[download]