Well, they're not added in free when you buy the pass - EXAMPLE: the 5 day PHP will cost you about $30 more than a 5 day PH - but they are not figured into the equation when you do an upgrade. The reason is the the difference in individual admission prices to the minor parks. Adult gate price admissions to Water Parks are $33.02, Pleasure Island is $21.25, and WWoS is $9.69. So there's no equitable way to value the unused minor parks.
But the major parks are all the same price. So what they do is base your entire ticket value for upgrading on the major park admissions. That way everyone gets the same formula for unused days. The plus options are considered just that, a "plus", and not part of the main ticket.
To answer the OP's question, if you trade in a ticket with left over unused plus options, you will lose those options entirely. There will be no extra dollar value credited for them.