What's a reverse cold water extraction? Do you just mean doing a normal CWE but keeping the insoluble stuff instead of the soluble stuff?
The amount of atropine in Lomotil is very tiny, too small to affect you when taken in normal doses, so I assume you want to remove it so you can take large quantities of the Lomotil without worrying about getting effects from the atropine? Taking too much Lomotil is not going to give you the same effects as Datura (Jimson Weed), but it could cause increased heart rate and make you feel sick. The 25 µg of atropine in each 2½ mg Lomotil tablet is 1/40 of the standard therapeutic dose of atropine via the oral route for normal anticholinergic uses. I've heard of people taking 40 tablets of Lomotil with only very minor side effects from the atropine, (definitely nothing remotely similar to Datura) but if you are planning on taking huge amounts of Lomotil it would be a good idea to try to remove the atropine.
Or were you planning to take the diphenoxylate by a non-oral route of administration?
I think that diphenoxylate is suposed to be barely soluble in water and atropine is very soluble in water, so in theory this should work. If your water was cloudy that may have just been that some of the diphenoxylate or any inactive ingredients in the pills got through the filter. I don't think that drying the stuff that remained in the filter is going to remove any more of the atropine. How much water did you use?