If the card deck runs out and must be reshuffled, do played end-of-game scoring cards and completed missions remain out of the deck, or are only discarded cards reshuffled?

Played end-of-game scoring cards and completed missions remain out of the deck; only discarded cards are reshuffled.

This is supported by the following:

When you play an end-of-game scoring card, you "keep it in front of you for the rest of the game" (page 15).
When you complete a mission (conditional or triggerable), you "keep all completed missions face down in front of you for the rest of the game" (page 15).
Only cards placed in the discard pile are available to be reshuffled: "After resolving the effect, place the card face up in a discard pile near the main deck, unless it is one of the types of cards described below" (referring to missions and end-of-game scoring cards, which are kept in front of you) (page 15).
When refilling the card row: "If the deck is ever empty, shuffle the discard pile to make a new deck" (page 19).

End-of-game scoring cards and completed missions are kept in front of you and are not placed in the discard pile.
Only the discard pile is reshuffled to form a new deck when the deck runs out.

Source: page 15, page 19

Source: Core Rulebook (pp. 15, 18, 19, 21, 7)

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