I was in contact with the developer but he seems to be busy recently so I am posting it here as well hoping other users may have an answer.
How does Princess do the phasing? This locus is not a particularly odd locus but in my brief manual inspection, I could not find non-contradicting sites so far.
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT LLsal Barry tanner Bond Klopp Brian
ssa01 139041651 0_24650 N <DEL> . PASS PRECISE;SVMETHOD=JASMINE;CHR2=ssa01;END=139043334;
0|1:0:DEL:.:8:2 0|1:0:DEL:.:8:20|1:0:DEL:.:8:20|1:0:DEL:.:8:20|1:0:DEL:.:8:20|1:0:DEL:.:8:2
#ssa01 139041651 0_24650 N <DEL> . PASS PRECISE;SVMETHOD=JASMINE;CHR2=ssa01;END=139043334;STD_quant_start=3.33542;STD_quant_stop=8.2991;Kurtosis_quant_start=1.31966;Kurtosis_quant_stop=2.30177;SVTYPE=DEL;RNAMES=4250ef10-dff4-4c5c-9c75-8ad085dcf7a9,43cd9070-cfef-48e3-af31-9ab39d2b93e7,49e571b9-1c82-405c-907e-f019f88f37de,8ba13242-89a8-46b0-8bbe-9ded59f71356,9674455c-0317-4798-9419-cb9e3c6db356,969e1d1e-d696-4d44-8c07-892fbfa14bd7,f6d1babd-83a1-4876-859b-0bff91cad0ce,f7a73e18-1dd5-4032-ac7e-55f61225e5c8;SUPTYPE=SR;SVLEN=-1683;STRANDS=+-;RE=8;REF_strand=1,1;AF=0.8;CONFLICT=0;OLDTYPE=DEL;IS_SPECIFIC=0;STARTVARIANCE=-4.000000;ENDVARIANCE=0.000000;AVG_LEN=-1683.000000;AVG_START=139041651.000000;AVG_END=139043334.000000;SUPP_VEC_EXT=111111;IDLIST_EXT=24650,24650,24650,24650,24650,24650;SUPP_EXT=6;SUPP_VEC=111111;SUPP=6;IDLIST=24650,24650,24650,24650,24650,24650;REFINEDALT=. GT:IS:OT:OS:DV:DR 0|1:0:DEL:.:8:2 0|1:0:DEL:.:8:2 0|1:0:DEL:.:8:2 0|1:0:DEL:.:8:2 0|1:0:DEL:.:8:2 0|1:0:DEL:.:8:2