Per the rules for SWU's:

"Limit of one one-way upgrade per certificate."

So I would guess that it depends on how the fare is calculated. If there is a separate fare for EBB-AMS and AMS-HNL after the long stopover, then you could use it on your choice of those two trips. And of course use the other SWU for the trip to EBB, as long as the fare is calculated as a "through fare". Can you provide the fare calculation that is being offered?