This single-line line relies only on awk and date to convert back and forth over timestamps:
awk 'BEGIN{FS=OFS=","}NR>1{au=$1 "," $2;t=$4; \ "date -u -d \""t"\" +%s"|getline ts; sum[au]+=ts;}END \ {for (a in sum){"date -u -d \"@"sum[a]"\" +%T"|getline h; print a,h}}' test.csv
having test.csv as follows:
Agent,Username,Project,Duration AAA,aaa,NBM,02:09:06 AAA,aaa,NBM,00:15:01 BBB,bbb,NBM,04:14:24 AAA,aaa,NBM,00:00:16 BBB,bbb,NBM,00:45:19 CCC,ccc,NDB,00:00:01
leads to:
CCC,ccc,00:00:01 BBB,bbb,04:59:43 AAA,aaa,02:24:23
You can use this with minor adjustments to extract the date from additional columns.