#!/bin/bash
s="value1,0021,value3,value4,
value1,00211,value3,value4,"
awk 'BEGIN{FS=OFS=","} {$2=sprintf("%06d", $2); $2=substr($2,1,2) gensub(/.{2}/,":&","g",substr($2,3))}1' <<< "$s"
IyEvYmluL2Jhc2gKcz0idmFsdWUxLDAwMjEsdmFsdWUzLHZhbHVlNCwKdmFsdWUxLDAwMjExLHZhbHVlMyx2YWx1ZTQsIgphd2sgJ0JFR0lOe0ZTPU9GUz0iLCJ9IHskMj1zcHJpbnRmKCIlMDZkIiwgJDIpOyAkMj1zdWJzdHIoJDIsMSwyKSBnZW5zdWIoLy57Mn0vLCI6JiIsImciLHN1YnN0cigkMiwzKSl9MScgPDw8ICIkcyI=
value1,00:00:21,value3,value4,
value1,00:02:11,value3,value4,