Your syntax looks a bit odd to me. I would code thusly (as personal preference):

foreach my $id ( sort keys %HoH ) {
    print ">$id: \n";
    
    
    for my $pos (  sort { $a <=> $b } keys %{$HoH{$id}} ) {  
        print "$pos:$HoH{$id}{$pos}\n";
    }
    print "\n";
}
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