My attempt to reproduce the behavior I described in https://github.com/genometools/genometools/issues/115.

gt-bug-115-desired-output.gff3

##gff-version   3
##sequence-region   PdomScaf0001 252075 255869
PdomScaf0001  maker	mRNA	252075	255869	.	-	.	ID=PdomMRNAr1.1-00022.1;_AED=0.29;_eAED=0.29;_QI=0|0.5|0.33|1|1|1|3|893|923
PdomScaf0001	maker	exon	252075	255370	118	-	.	Parent=PdomMRNAr1.1-00022.1
PdomScaf0001	maker	stop_codon	252968	252970	.	-	.	Parent=PdomMRNAr1.1-00022.1
PdomScaf0001	.	CDS	252968	255370	.	-	.	ID=myCDS;Parent=PdomMRNAr1.1-00022.1
PdomScaf0001	maker	exon	255453	255790	35.2	-	.	Parent=PdomMRNAr1.1-00022.1
PdomScaf0001	.	CDS	255453	255790	.	-	.	ID=myCDS;Parent=PdomMRNAr1.1-00022.1
PdomScaf0001	maker	exon	255839	255869	9.8	-	.	Parent=PdomMRNAr1.1-00022.1
PdomScaf0001	.	CDS	255839	255869	.	-	.	ID=myCDS;Parent=PdomMRNAr1.1-00022.1
PdomScaf0001	maker	start_codon	255867	255869	.	-	.	Parent=PdomMRNAr1.1-00022.1
###

gt-bug-115-input.gff3

##gff-version   3
##sequence-region   PdomScaf0001 252075 255869
PdomScaf0001  maker	mRNA	252075	255869	.	-	.	ID=PdomMRNAr1.1-00022.1;_AED=0.29;_eAED=0.29;_QI=0|0.5|0.33|1|1|1|3|893|923
PdomScaf0001	maker	exon	252075	255370	118	-	.	Parent=PdomMRNAr1.1-00022.1
PdomScaf0001	maker	stop_codon	252968	252970	.	-	.	Parent=PdomMRNAr1.1-00022.1
PdomScaf0001	maker	exon	255453	255790	35.2	-	.	Parent=PdomMRNAr1.1-00022.1
PdomScaf0001	maker	exon	255839	255869	9.8	-	.	Parent=PdomMRNAr1.1-00022.1
PdomScaf0001	maker	start_codon	255867	255869	.	-	.	Parent=PdomMRNAr1.1-00022.1
###

gt-bug-115.c

#define WITHOUT_CAIRO
#include "genometools.h"

int main(int argc, const char **argv)
{
  GtArray *nodes;
  GtError *error;
  GtFile *outfile;
  GtNodeStream *gff3in, *arrayoutstream, *arrayinstream, *gff3out;
  gt_lib_init();

  gff3in = gt_gff3_in_stream_new_unsorted(1, &argv[1]);
  gt_gff3_in_stream_check_id_attributes((GtGFF3InStream *)gff3in);
  gt_gff3_in_stream_enable_tidy_mode((GtGFF3InStream *)gff3in);

  error = gt_error_new();
  nodes = gt_array_new( sizeof(GtGenomeNode *) );
  arrayoutstream = gt_array_out_stream_new(gff3in, nodes, error);

  int result = gt_node_stream_pull(arrayoutstream, error);
  if(result == -1)
  {
    fprintf(stderr, "error processing node stream: %s", gt_error_get(error));
  }
  gt_node_stream_delete(gff3in);
  gt_node_stream_delete(arrayoutstream);

  GtUword i;
  for(i = 0; i < gt_array_size(nodes); i++)
  {
    GtGenomeNode **gn = gt_array_get(nodes, i);
    GtFeatureNode *fn = gt_feature_node_try_cast(*gn);
    if(fn == NULL)
      continue;

    GtStr *seqid = gt_genome_node_get_seqid(*gn);
    GtGenomeNode *cdspart3 = gt_feature_node_new(seqid, "CDS", 252968, 255370, GT_STRAND_REVERSE);
    GtGenomeNode *cdspart2 = gt_feature_node_new(seqid, "CDS", 255453, 255790, GT_STRAND_REVERSE);
    GtGenomeNode *cdspart1 = gt_feature_node_new(seqid, "CDS", 255839, 255869, GT_STRAND_REVERSE);
    gt_feature_node_make_multi_representative((GtFeatureNode *)cdspart3);
    gt_feature_node_set_multi_representative((GtFeatureNode *)cdspart2, (GtFeatureNode *)cdspart3);
    gt_feature_node_set_multi_representative((GtFeatureNode *)cdspart1, (GtFeatureNode *)cdspart3);
    gt_feature_node_add_child(fn, (GtFeatureNode *)cdspart1);
    gt_feature_node_add_child(fn, (GtFeatureNode *)cdspart2);
    gt_feature_node_add_child(fn, (GtFeatureNode *)cdspart3);
    gt_feature_node_set_attribute((GtFeatureNode *)cdspart3, "ID", "myCDS");
  }

  GtUword progress = 0;
  arrayinstream = gt_array_in_stream_new(nodes, &progress, error);

  outfile = gt_file_new_from_fileptr(stdout);
  gff3out = gt_gff3_out_stream_new(arrayinstream, outfile);
  gt_gff3_out_stream_retain_id_attributes((GtGFF3OutStream *)gff3out);

  result = gt_node_stream_pull(gff3out, error);
  if(result == -1)
  {
    fprintf(stderr, "error processing node stream: %s", gt_error_get(error));
  }

  gt_file_delete_without_handle(outfile);
  gt_node_stream_delete(arrayinstream);
  gt_node_stream_delete(gff3out);
  gt_array_delete(nodes);
  gt_error_delete(error);
  gt_lib_clean();
  return 0;
}