The Royal Mint indicated that the technology is patented, and having relatively few patents under its name it seems likely that they are tagging their coinage with embedded luminescent particles.

Abstract:

Formation of an authentication element by deposition of a metal layer with embedded particles on a metal substrate, wherein the embedded particles are configured to convert energy from one wavelength to another. The embedded particles may be upconverters, downconverters, or phosphorescent phosphors, which can be detected and measured with analytical equipment when deposited in the metal layer. A metal substrate may include coinage.

Essentially they are embedding inorganic fluorescent compounds into the metal plating on the coin. When a certain spectrum of light is shone on the coin, these particles absorb that energy and emit a different spectrum. So, depending on the particle they embed, the detector may be as simple as a UV LED and a light sensor at a specific wavelength.

By integrating different ratios of different particles they can differentiate between different coins, for instance.

Further, the patent explains that the plating process generally includes many layers of plating. They can add different mixes at each layer, and thus tell how well-used a coin is, by how many of the upper layers are removed. Aging the coin can be useful to determine when to take it out of circulation before these particles are entirely removed.

This technology can also be used in automotive parts, and technology equipment to defeat counterfeiting. For instance if you replace your iPhone screen with a counterfeit part, unless the counterfeiter goes to the trouble of matching the exact luminescent profile, Apple may be able to detect that you broke your phone's warranty, should Apple choose to use such technology to protect themselves from counterfeit products.

The technology doesn't include any sort of serial number or tracking component, so tracking coins through the system is unlikely, but perhaps other techniques they apply to the coins could be used for that purpose.