"Scrap Token" and "Scrap Cost" are obsolete terms from an earlier version of Chronicle X, but which have managed to dodge the proofreading and survived in the text on a few cards, perhaps most notably the two Space Station cards "Store Closet" and "Workshop".
In most cases, the simplest fix is to read "Resource(s)" where it says "Scrap Token(s)" and "Resource Cost" where it says "Scrap Cost".
Upgrade
This page describes upgrading Items and the Space Station for the Hero Players. For Overmind Player upgrades, see Upgrade Nodes.
During the Resolution Phase, the Hero Players may spend Resources to Upgrade Items. Upgrading an Item is only possible for items that have an Advanced form; those Item cards are double sided, and have the Basic form of the Item on one side, and the Advanced form on the other side. (The sides are distinguished by the Advanced form having the word "Advanced" first in the Item name.)
All Items have one or more Resource icons in their middle area, between the image and the text box. Each Resource icon has a number next to it, indicating how many Resources of that type it is worth.
Upgradeable Items also have an icon with two arrow heads pointing up next to the Resource icons, to indicate the Item is upgradeable; and for those Items, the Resource icons indicate the upgrade cost. For non-upgradeable Items, the Resource icons indicate the Resource value. To Upgrade an Item, discard non-upgradeable Items and/or Resource tokens of enough combined Resource value to cover the upgrade cost. Then flip the upgraded Item over to the Advanced side.
If the discarded Items generated more Resource value than what was needed to pay for the upgrade, you get change back in the form of Resource tokens.
The Hero Players may generally only upgrade units during the Resolution Phase, not during an ongoing Mission; although special abilities may allow exceptions.
Space Station Upgrades
During the Resolution Phase, the Heroes can spend also Resources to extend their Space Station. All Space Station room cards except the two starter ones ("HQ" and "Warehouse") have a Resource cost marked on them, which is paid to build the room. Heroes can freely move between any Space Station rooms that have been built, although some rooms sets a limit (specified on the card) on how many Heroes may use the room at the same time.