Hey alexlounsbury, I know its been a while but here is a paper from Megger that discusses your exact problem:
Effects of Low Resistance Measurement Instruments on Protection and Control Devices, Effect of DLRO on the differential protection scheme
The DC current used for measuring the low resistance can affect the protection and control circuitry in adverse ways. Typical problems encountered are Current Transformer (CT) magnetization, accidental tripping of differential relays and inconsistent and unreliable low resistance measurements. The paper will address the root cause of these encountered problems. It will recommend precautions to take prior to performing the test and discuss in detail the recommended practices to avoid any misoperation of connected protection and control devices.
https://content.megger.com/getattach...ol-Devices.pdf