Stencil Cleaners- Sn/Pb & Pb Free

What is the common practice for cleaning Tin/Lead and Lead Free solderpaste on stencils- some machines have filtration I'm told, so its not an issue according to the mfrs. On machines that don't have filtration do you run one after the other? Do you drain and flush? I figure the solder sphere's will settle to the bottom and not cross-contaminate, right, wrong?

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