The dipstick used to check the fluid level is not meant to go all the way down the tube. Although the fluid may look nasty to you, MB does not recommend changing it. When I R&R'd the trans cooler lines on my own '99 ML320, the fluid that I drained out was indeed discolored but I put it back in along with 1/2 quart of fresh stuff when I refilled the tranny.

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Regards,
Aaron