Why not just use the sep funnel for draining off the base soup, leaving only the solvent behind? (instead of turkey baster -> sep funnel) Unless you only have a small sep funnel, in which case I understand.
When working with the sep funnel, I run hot water over it, or leave it in a hot water bath. This way the base soup runs down to the bottom, off the sides. If you do this, be sure to release the pressure as the solvent expands and gases. If you don't release the pressure, the stopcock can shoot off.
I clean my funnel with HOT water, I rinse it through and through. Concerning what could be left in the funnel, well, I shouldn't think it could be that significant after the 3rd or 4th pull anyway.
I like things clean and trace free.
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