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Differential probe is not needed. Scope in general is not for accurate measurements. Use multimeter. I'm not sure what exactly you try to measure and what is your goal, but in this case I would measure voltage drop from LDO output up to the IC pins of interest. Don't forget that there will be some drop on the return path too (GND). Return path drop is usually less, because ground is typically distributed by massive copper planes and has less resistance. So total supply drop will be the sum of those.
You could make handy widget with an instrumentation amp.A micropower like a $3 INA33 it has an input offset of 10uV, an error of 1% in 1mV.Set gain to 100 and chuck it in the draw. It will run for thousands of hours from a couple of AAs .A practical circuit is attached.