Thanks folks, think I've got it.
One more situation, just to make sure we're rock solid.
Flenta, from the Fighter CD, starts with 3 Spells but has no Arcane or Divine skill. All but one spell (Masterwork) are banished anytime she uses them.
For the sake of this situation, let's assume she uses (banishes) all of her spells each scenario. The fighter deck is pretty short on spells to choose from. For Base and AD1:
B - Strength - Basic
B - Call Weapon - Elite
1 - Obscure
1 - Speed
First, unless she uses an upgrade or reward she is always going to go through the hierarchy and grab first Strength, then Call Weapon, then Obscure or Speed from her box even if the party acquired a dozen spells during the scenario. Even if she uses an upgrade she is still going to be stuck with Strength and Call Weapon as her only fill-in options.
Second, unless she uses an upgrade every scenario she will never be able to advance her deck beyond that hierarchy, assuming the party acquires an AD2 or greater spell each scenario. Meaning she would have to choose from "upgrading" a spell each scenario just to maintain her previous deck level or revert to those same hierarchy spells if she wanted to upgrade any other part of her deck (Weapon, Armor, Item, Ally, Blessing). Also meaning, unless she gains some form of additional reward upgrade, (before she starts Adventure 4) she will not be able to have more than one spell in her deck that is above AD1.