How about killing the power to the system and using the primary anode plus a third electrode to take pertinent measurements?
Suppose you're taking two-electrode measurements. One electrode is already in use and the other is reserved for measurements. If you
use a floating power supply for the measurements, you don't have to turn off the main supply. The only real requirement is to ensure that your
measuring apparatus has high impedance so it doesn't become (much) of a parallel current path or affect the measurement too much.
But this issue is premature. The first thing to do is to take some trial measurements in a test rig and figure out what the right correlations are.
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