There’s so many factors involved in this hypothetical situation, but when looking at it as a “price per year” problem, new could be more economical than used despite upfront cost. Don’t forget that the core module contains components, like flash storage, that are prone to wear-and-tear. Where a new upgraded core module will give you N years of life, a used, refurbished one would in the common case have a life expectancy of N minus its previous lifetime.
Anyway, this discussion is virtually meaningless as long as SoCs aren’t pin-compatible with predecessors. Which is unlikely when components on the SoC reshuffle to optimise the very last milliwatt of power consumption out and as old technology (USB 2.0, 4G antenna, LPDDR3, MIPI DSI) makes place for newer or more desirable technology (USB-C, 5G antenna, LPDDR4, eDP) with different physical characteristics. Pins required to drive the current set of selected peripherals might have disappeared, or extra pins might have introduced for supporting newer standards that cannot be routed to older peripherals because they don’t have the pogo-pins for it.
It isn’t even a given that the other modules currently shipped in the Fairphone 2 would meet the electronical requirements to be compatible with a newer chip. Changes in the external characteristics of the chip resulting from production at a different procedure could well raise resistance, line delay, parasitic capacitance or current leakage to prohibitive levels even when trying to run these peripherals at the same speed. Whatever the reason, it’s not uncommon for newer versions of a standard (like USB) to place stricter physical requirements on peripheral compatibility than their predecessor - which could snowball a project from upgrading an SoC into upgrading the whole design of the device.