If you want an accurate assessment of what's going on, you need to get rid of the previous sample, so yes, clean the plates.
The main things are to use clean plates and plenty of samples. If you can completely fill the sample area that's good. But if you've got 3/4 of it filled, you can still scan. I've managed to scan with much less. It changes the base current the generator reads, just like differing using tens pads in differing patterns does.
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