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I use the same funnel for getting used oil back in the jugs, new oil in the engine, and whatever other oil into other things that the funnel fits.
I just let it all drain out each use, and wipe any residual waste oil out before using it for new oil. A little bit of engine oil in the fuel tank won't hurt anything. power service is pretty thin, the little traces that might be left after you wipe the funnel couldn't be enough to do anything once mixed in with the engine oil. I wouldn't worry about it at all.