If the pilots use GpsDump to upload the waypoints there is a simpler way for you.
Use the following format of the waypoint file:
$FormatGEO
BRA055 N 47 49 45.96 E 011 07 40.14 550 BRAEUNIGER
HV1042 N 59 30 16.98 E 009 59 49.98 425 HV101 GR-TTERUD S
HV1032 N 59 28 58.02 E 010 04 12.00 325 HV102 GLANEBERGET
COM000 N 04 05 06.00 E 001 02 03.00 0 COMPID
The 3 first waypoints are examples. The last waypoint denotes a COMPID of 123456. If your original waypoint list is in a different format the geo format can easily be generated by GpsDump.