When I used home-made soylent, I first put in (all) the water, then the powder. My shaker also has a plastic grid inset in the lid. Putting in the water first also lets you see exactly how much water you have (transparent measuring cup shaker). I don't remember ever having any problems.
Personally I'm more interested in knowing how much powder I have than how much water. (Though I'm not sure how accurate I can really be based on the volume markings - weight would be more accurate, but also a hassle.)
A small amount of water seems to work, though it does increase uncertainty in powder volume a bit.
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