Actually they are both correct in this case. There are two separate issues: booking the ticket in original class of service, and applying the eVip.

The EXP desk told your friend that you have to do the original booking. Your friend cannot upgrade a booking that doesn't exist. Once there is a booking you or her can call and apply the evip using the account number from which the evip are pulled (and additional tax, if any must be collected as well).

That is the reason why I suggested earlier that you will do the whole thing in one call yourself. You can be confirmed right away, you don't need to call your friend and have her waste more time with a second agent, and you pay for the ticket and any additional tax for upgrade together.