The Individually Powered Dipole (IPD) and Individually Powered Quadrupole (IPQ) magnets of the Large Hadron Collider (LHC) at CERN are protected by a dedicated Quench Detection System (QDS). Within the scope of the High Luminosity LHC (HL-LHC) upgrade, the radiation level in the designated installation area will increase up to 25 Gy per year exceeding the radiation tolerance level of the existing system. In order to reinforce its radiation tolerance as well as its functionality, this protection system has been upgraded to withstand in enhanced luminosity. A radiation tolerant linear power supply has been developed to replace commercial switch mode devices. The design is based on tested Commercial-Off-The-Shelf (COTS) electronic components and takes advantage of an innovative, thermally efficient layout. At present, two power supplies are ensuring redundancy but no electrical separation from the magnet, thus galvanic isolation is implemented in the upgraded system parts. These comprise the universal magnet quench detector cards, the current leads and bus-bar splices quench detection cards. They use Field Programmable Gate Arrays (FPGAs), where the quench detection algorithms are implemented. Additionally, a quench heater supervision system is present in the crate for integrity monitoring. The quench protection system is completed with the new, radiation tolerant, and fieldbus communication controller that provides enhanced diagnostics capabilities. The entire system has been recently successfully evaluated under radiation at the CERN High Energy Accelerator Mixed Field (CHARM) facility. This article describes the design and implementation of the new protection unit as well as the associated radiation qualification.