No, it is optional to remove each non-blessing boon.

Resolution: On page 8 of the Guide, in Build the Vault, replace the first paragraph with:

Starting with Season 6, each adventure includes rules for building the vault. In earlier seasons, each adventure lists the products that adventure requires. To build the vault for a scenario in one of those adventures, start by adding all of the cards from the listed products to the vault, then remove all Basic and Elite banes whose level is at least three lower than the # of the adventure, and you may remove any non-blessing boons that fit that criteria. For example, if you’re setting up a scenario in adventure 5, you’ll remove all Basic and Elite banes of levels 0 (that is, B, P, and C), 1, and 2, and you may remove any non-blessing Basic or Elite boons of those levels. If you don’t have time to remove those cards in advance, you can remove them as you find them—when you come across one, just replace it with another card of the same type from the vault. Ignore any instructions on the Adventure Path card related to banishing Basic and Elite cards.